# pos

id: cord-291729-4l4v9jxd
pos: NNP
token:
  https://www.fda.gov/newsevents/press-announcements/coronavirus-covid-19-update-fda-issues-first-emergencyauthorization-sample-pooling-diagnostic

lemma:
  https://www.fda.gov/newsevents/press-announcements/coronavirus-covid-19-update-fda-issues-first-emergencyauthorization-sample-pooling-diagnostic


# ent

id: cord-030061-55ntc4wj
type: CELL_TYPE
entity:
  allogeneic hematopoietic stem cell transplantation 77 recipients Clinical features of fatal severe fever with thrombocytopenia syndrome 79


id: cord-270947-6e5cw2q9
type: DISEASE
entity:
  influenza A virus FluA influenza B virus respiratory syncytial virus human metapneumovirus and adenovirus Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay RESULTS Twenty studies of 5510 patient samples were eligible for analysis Multiplex PCRs demonstrated high diagnostic accuracy with area under the receiver operating characteristic curve AUROC equal to or more than 0 98 for all the above viruses except for adenovirus AUROC 0 89 FilmArray Verigene RV


id: cord-325186-nq6ay4eo
type: ORG
entity:
  the European Society of Clinical Microbiology and Infectious Diseases Using Procalcitonin to Guide Antibiotic Therapy


id: cord-253250-zet48zcl
type: ORG
entity:
  the World Association for Infectious Diseases and Immunological Disorders WAidid Global Tuberculosis Network


id: cord-257696-ybu772zw
type: WORK_OF_ART
entity:
  Dexamethasone in Hospitalized Patients with Covid 19 Preliminary Methylprednisolone as Adjunctive Therapy for Patients Hospitalized With COVID 19


id: cord-279111-jaa45kyc
type: DISEASE
entity:
  respiratory symptoms Influenza virus human parainfluenza viruses 1e4 and respiratory syncytial virus


id: cord-257248-aii0tj9x
type: PROTEIN
entity:
  Streptococcus pneumoniae nontypeable Haemophilus influenzae NTHi Moraxella catarrhalis Staphylococcus aureus Bordetella


id: cord-257248-aii0tj9x
type: TAXON
entity:
  adenovirus human metapneumovirus human coronaviruses OC43 229E NL63 HKU1 human bocavirus enterovirus


id: cord-334835-j6u8t8j2
type: DISEASE
entity:
  hypertension obesity liver cirrhosis chronic neurological 211 disorder active cancer dementia dyspnoea confusion


id: cord-278807-p1crrb8n
type: DISEASE
entity:
  influenza A H1N1 pandemic wave on the pattern of hibernal respiratory virus epidemics Relationships between A H1N1 pdm09 influenza infection


id: cord-294546-0otd1heg
type: PROTEIN
entity:
  Prendki V Huttner B Marti C Mamin A Fubini P E Meynet M P Scheffler M Montet X Janssens J P Reny J L Kaiser L Garin N Stirnemann J title Accuracy


id: cord-343090-dsjq98ks
type: CHEMICAL
entity:
  cobicistat NCT04252274 2 on human stem cells transfusion 312 ChiCTR2000029606 ChiCTR2000030944 1 testing hydroxycholoroquine


id: cord-283818-4m9p717r
type: PROTEIN
entity:
  S47 Rh A 1 S48 RhA 2 S49 Rh B 1 S50 RhB 2 S51 Rh C 1 S56 Klebsiella pneumoniae S57 Streptococcus pneumoniae S58


id: cord-283818-4m9p717r
type: DNA
entity:
  S gene 3822bp F3 outer forward primer B3 outer backward primer FIP forward inner primer BIP 52 backward inner primer LF loop forward primer Bat


id: cord-294392-a8s66g96
type: DISEASE
entity:
  hypertension cardiovascular disease diabetes cerebrovascular disease chronic obstructive pulmonary 90 disease


id: cord-297625-eby014gm
type: DISEASE
entity:
  metapneumovirus coronavirus 229E HKU1 OC43 NL63 respiratory syncytial virus A B picornavirus and parainfluenza virus 1 2 3 A


id: cord-333334-90q1xkld
type: ORG
entity:
  the Department of Pulmonary and Critical Care Medicine Department of Traditional Chinese Medicine Lung Disease


id: cord-333334-90q1xkld
type: DISEASE
entity:
  influenza A H1N1 H7N9 virus influenza B virus respiratory syncytial virus parainfluenza virus adenovirus EpsteineBarr virus herpes simplex


id: cord-300023-2dg7njki
type: DISEASE
entity:
  influenza A H1N1 pdm09 virus on 4 household surfaces Efficacy of soap and water and alcohol based hand rub preparations


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  Panton Valentine leukocidin toxin L Faraj L A S Snyder N J Loman D P Turner M J Pallen D Ala Aldeen R James Nottingham Birmingham UK


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  J Broomhall C McCowan S Gonzalez McQuire K Akhras S Merchant P Davey Dundee High Wycombe UK Raritan US


id: cord-009664-kb9fnbgy
type: CELL_TYPE
entity:
  liver bacterial cells 3 63 and 4 99 log10 cfu g pNS and for lung bacterial cells 2 56 and 4 22 log10 cfu g pNS Conclusions Allogeneic transplantation with PBMCs


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  H3 influenza B Flu B Respiratory syncytial virus RSV subtypes A and B Adenovirus AdV Parainfluenza 1 PIV 1 Parainfluenza 2 PIV 2 Parainfluenza 3 PIV 3 human metapneumovirus hMPV and


id: cord-009664-kb9fnbgy
type: DNA
entity:
  AbaR1 associated genes positive strains aacC1 21 aadA1 21 aadB 4 aphA1 21 strA 3 merA 20 tetA 18 cat 23


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  Consorte G Congedo L Cosentino D D Antonio L Pippa L Manzoli C Granchelli Pescara Chieti IT Objectives A large prospective cohort


id: cord-009664-kb9fnbgy
type: DISEASE
entity:
  herpes simplex virus 1 and 2 HSV1 2 human parechovirus HPeV cytomegalovirus CMV Epstein Barr Virus EBV enterovirus EV


id: cord-019490-m1cuuehi
type: CELL_LINE
entity:
  gastritis GT duodenal ulcer DU and gastric ulcer GU and gastric cancer GCA patients were 41 2 57 9 and 70 6


id: cord-019490-m1cuuehi
type: PROTEIN
entity:
  monoclonal FemtoLab H pylori Connex Martinsried Germany and a polyclonal Premier Platinum HpSA Meridian Diagnostics Inc Cincinnati USA stool antigen


id: cord-019490-m1cuuehi
type: PROTEIN
entity:
  HHV 6B D Becker S Ziegelmaier S Wach T Laue T Grewing Hamburg D Objectives Human herpesvirus 6 HHV 6


id: cord-019490-m1cuuehi
type: DNA
entity:
  neonatal intensive care unit N Ben Saida A Ferjani J Boukadida Sousse TN Objective Methicilllin resistant Staphylococcus haemolyticus MRSH


id: cord-019490-m1cuuehi
type: PROTEIN
entity:
  coagulase negative Staphylococci 13 5 Pseudomonas aeruginosa 12 2 Enterobacter cloacae 7 2 Klebsiella pneumoniae 5 7


id: cord-019490-m1cuuehi
type: CELL_LINE
entity:
  J Passarell B Cirincione S Van Wart K Liolios T Babinchak E J Ellis Grosse P Ambrose Buffalo Collegeville Albany USA Objectives Tigecycline T the


id: cord-019490-m1cuuehi
type: GGP
entity:
  cefixime H Derendorf P Liu K Rand B Obermann Gainesville USA Munich D Objectives Pharmacokinetic PK Pharmacodynamic PD modeling of antibiotics


id: cord-019490-m1cuuehi
type: SO
entity:
  RealArt HHV 6 A B LC PCR assay has the same temperature profile as the RealArt LC PCR assays for HSV1 2 EBV CMV


id: cord-019490-m1cuuehi
type: GGP
entity:
  Pseudomonas aeruginosa 8 Staphylococcus epidermidis 7 Escherichia coli 7 Staphylococcus aureus 6 Streptococcus viridans 6 Klebsiella pneumoniae 4 Enterococcus faecalis 4


id: cord-019490-m1cuuehi
type: DISEASE
entity:
  coronary heart disease atrial fibrillation hypertension obstructive pulmonary disease renal insufficiency cardiomyopathy


id: cord-023592-w96h4rir
type: GGP
entity:
  Meropen 8 9 2 3 1 1 11 12 7 7 3 3 11 12 7 11 4 9 8 12 7 12 5 12 Ceftriax 4 6 1 2 0 0 8 12 5 7 3 3 9 12 9 12 6 10 11 12 8 12 4 10 Moxi 1 5 8 0 1 0 0 8 10 4 6 1 2 9 10 8 10 5 9 10 10 8 10 7 10 Levo 1 5 5 0 0 0 0 8 10 4 6 1 1 10 10 8 10 3 6 9 10 9 10 5 10 Gati 1 4 6 0 1 0 0 7 10 2 7 1 1 10 10 6 10 3 7 9 10 8 10 4 9 Azithro 2 1 1 0 0 0 0 1 1 1 1 1 1 2 2 1 2 1 2 2 2 2 2 2 2


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  MgCl 2 3 mM M and 0 5 lM M of each primer The region amplified belongs to the hexon gene Total processing time


id: cord-023592-w96h4rir
type: DISEASE
entity:
  postoperative infections A Artero J J Camarena R Zaragoza S Sancho J Tamarit R González J Nogueira Valencia E


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  clavulanate imipenem meropenem ceftriaxone cefuroxime cefpodoxime cefdinir ciprofloxacin levofloxacin gatifloxacin moxifloxacin azithromycin clarithromycin


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  imipenem meropenem ceftriaxone moxifloxacin levofloxacin gatifloxacin azithromycin clarithromycin vancomycin teicoplanin


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  ampicillin cephalothin cefuroxime piperacillin tazobactam amoxicillin clavulanic acid ceftazidime cefotaxime imipenem aztreonam gentamicin streptomycin chloramphenicol tetracycline nalidixic acid trimethoprim sulfamethoxazole


id: cord-022501-9wnmdvg5
type: DNA
entity:
  3GCs 49 2 site 3 vs 24 4 sites 1 2 4 5 p 0 001 and Glycopeptides 31 8 site 1 vs 9 3 site 2 3 4 5 p 0 001


id: cord-022501-9wnmdvg5
type: PROTEIN
entity:
  methicillin resistant S aureus IBS 3284 CMI 1 5 mg L producing Enterotoxin A Panton Valentine leucocidin


id: cord-022501-9wnmdvg5
type: DNA
entity:
  II 750 bp aadB 2000 bp oxa30 aadA1 III 900 bp carb2 1100 aadA1 IV 1500 bp dfrA1 aadA1 V and VI 2000 bp


id: cord-022501-9wnmdvg5
type: DNA
entity:
  chloramphenicol 36 6 tetracycline 34 2 amoxicillin clavulanic acid 32 4 trimethoprim sulfamethoxazole 2 3 gentamicin 1 6 and cefotaxime 0 8 Ciprofloxacin


id: cord-022501-9wnmdvg5
type: DNA
entity:
  Danish cohort 43 tcdA tcdB cdtA cdtB 107 tcdA tcdB cdtA cdtB and 24 non toxigenic tcdA tcdB cdtA cdtB


id: cord-022501-9wnmdvg5
type: DNA
entity:
  enterococcal surface protein esp hyaluronidase variant gene hylEfm and E faecalis antigen A variant efafm Objectives


id: cord-022501-9wnmdvg5
type: CELL_LINE
entity:
  IMAM KHOMEINI hospital Tehran SAHID Dr BAHONAR hospital Kerman divided by random blocks to outpatient or inpatient therapy received two 1 g doses of intramuscular ceftriaxone at 24 hour intervals while hospitalized then were discharged and reevaluated within 48 72 hours or remained hospitalized until afebrile for 48 hours All patients completed a 14 day course of oral cephalexin We performed urine cultures


id: cord-022501-9wnmdvg5
type: PROTEIN
entity:
  S Coagulase negative 40 S aureus 22 and Enterococcus 11 Late prosthetic valve endocarditis involved S viridans 30 S Coagulase negative 17 and S aureus 13 Transesophageal echocardiography


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  N 2 4 chlorophenoxymethyl benzoyl N 2 6 dichloro phenyl thiourea and N 2 4 chlorophenoxymethyl benzoyl N 4 bromo phenyl thiourea


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  dalfopristin clindamycin ciprofloxacin levofloxacin gentamicin streptomycin erythromycin telithromycin


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  ampicillin amoxicillin clavulanic acid cefotaxime gentamicin chloramphenicol tetracycline trimethoprim sulfamethoxazole


id: cord-022501-9wnmdvg5
type: DISEASE
entity:
  SARS coronavirus SARS CoV like virus in non caged wild animals from the wild of Hong Kong Special Administrative Region


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  S mitis n 2 S parasanguinis n 1 and S salivarius or S vestibularis n 1 Moreover the pyrograms of three blood


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  imipenem meropenem cefotaxime ceftazidime cefepime aztreonam amikacin tobramicin ciprofloxacin ofloxacin


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  beta lactams penicillin amoxicillin amoxicillin clavulanic acid cefepime cefuroxime ceftriaxone imipenem


# url

id: cord-291729-4l4v9jxd
domain: www.fda.gov
url:
  http://www.fda.gov/newsevents/press-announcements/coronavirus-covid-19-update-fda-issues-first-emergencyauthorization-sample-pooling-diagnostic


# bib

id: cord-008258-5v55vv4s
title: Is it the end of the nervous breakdown on avian influenza?
author: Raoult, D.
date: 2015-06-21
txt: ./txt/cord-008258-5v55vv4s.txt
cache: ./cache/cord-008258-5v55vv4s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130003/
doi: 10.1016/j.cmi.2015.06.011
abstract: nan
summary:
  The nervous breakdown on avian influenza that has affected the WHO, the different governments and the largest journals in the world may perhaps end with two articles published in the Journal of Infectious Diseases in May 2015 [1, 2] . This prospective survey in Egypt over 3 years on 1000 people showed that when H5N1 was endemic, 2% of the exposed population had antibodies compared with 0% of controls, and when the epidemic H9N2 appeared in poultry, seroprevalence increased from 0 to 5.6% and 7.5%, all asymptomatic infections. In total the zoonotic variant of H5N1 avian flu and H9N2 is very common in people in contact with poultry; it is banal and most of the time, asymptomatic. Avian influenza A(H5N1) and A(H9N2) seroprevalence and risk factors for infection among Egyptians: a prospective, controlled seroepidemiological study


id: cord-009295-4c0zwhdh
author: Bal, A.
date: 2020-03-28
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142683/
doi: 10.1016/j.cmi.2020.03.020
abstract: nan
title:
  Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del)


id: cord-009664-kb9fnbgy
title: Oral presentations
author: nan
date: 2014-12-24
txt: ./txt/cord-009664-kb9fnbgy.txt
cache: ./cache/cord-009664-kb9fnbgy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162236/
doi: 10.1111/j.1469-0691.2009.02857.x
abstract: nan
summary:
  Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically.


id: cord-009675-utz0iazs
title: Are point‐of‐care (POC) virological tests what is needed?
author: Madeley, C. R.
date: 2007-06-05
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162335/
doi: 10.1111/j.1469-0691.2007.01738.x
abstract:
  Point‐of‐care (POC) tests are becoming more available, although the way in which they should be used is currently undecided. Any ‘laboratory’‐based diagnosis of respiratory infections has three components: the specimen taken, the test used, and the interpretation of the results. Each of these components needs to be carefully addressed when using POC tests for the diagnosis of respiratory tract infections. Given the enthusiasm with which POC tests are being developed, it is likely that they will be used more and more widely. If so, the advantages and limitations of their use should be fully discussed and the implications recognised.


id: cord-010162-hfo35gsq
title: Atypical respiratory pathogens
author: Saikku, Pekka
date: 2014-12-29
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172217/
doi: 10.1111/j.1469-0691.1997.tb00464.x
abstract:
  The main atypical pathogens in respiratory tract infections are classified on the basis of their ability to cause atypical pneumonia. This is not a well-defined clinical entity, and it is evident that atypical pathogens can sometimes cause ‘typical’ pneumonias and vice versa. This emphasizes the need for microbiological diagnosis, since it affects the selection of proper treatment, in which β-lactam antibiotics and aminoglycosides are not effective. Moreover, mixed infections caused by atypical and typical pathogens together are common. At this moment rapid and sensitive diagnostic methods are lacking. Besides numerous viruses, the main bacterial pathogens causing atypical pneumonias are Mycoplasma pneumoniae, two chlamydial species, Chlamydia pneumoniae and C. psittaci, one rickettsia, Coxiella burnetti, and several Legionella species. The majority of these pathogens cause upper respiratory tract infections more often than overt pneumonias. An atypical agent, Chlamydia pneumoniae, has also been associated with chronic inflammatory conditions in the cardiovascular system. The most recently discovered pathogen in atypical pneumonias is a hantavirus causing hantavirus pulmonary syndrome.


id: cord-019490-m1cuuehi
title: Abstracts cont.
author: nan
date: 2015-12-28
txt: ./txt/cord-019490-m1cuuehi.txt
cache: ./cache/cord-019490-m1cuuehi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129916/
doi: 10.1111/j.1469-0691.2005.clm_1134_02.x
abstract: nan
summary:
  Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control.


id: cord-022501-9wnmdvg5
title: P1460 – P1884
author: nan
date: 2015-12-28
txt: ./txt/cord-022501-9wnmdvg5.txt
cache: ./cache/cord-022501-9wnmdvg5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/
doi: 10.1111/j.1470-9465.2006.12_4_1431.x
abstract: nan
summary:
  Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing).


id: cord-023592-w96h4rir
title: Abstracts cont.
author: nan
date: 2015-12-28
txt: ./txt/cord-023592-w96h4rir.txt
cache: ./cache/cord-023592-w96h4rir.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172567/
doi: 10.1111/j.1469-0691.2004.0902c.x
abstract: nan
summary:
  Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined.


id: cord-031493-w8agvg9g
title: Possible therapies of Post-COVID-19 chronic symptoms()
author: Davido, Benjamin
date: 2020-09-06
txt: ./txt/cord-031493-w8agvg9g.txt
cache: ./cache/cord-031493-w8agvg9g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474820/
doi: 10.1016/j.cmi.2020.09.001
abstract: nan
summary:
  key: cord-031493-w8agvg9g authors: Davido, Benjamin; Seang, Sophie; Barizien, Nicolas; Tubiana, Roland; de Truchis, Pierre title: Possible therapies of Post-COVID-19 chronic symptoms() date: 2020-09-06 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.001 sha: doc_id: 31493 cord_uid: w8agvg9g nan responsible for dysautonomia in patients with persistent symptoms following acute SARS-23 COV2 infection. Physicians must keep in mind that COVID-19 is not only a disease 24 responsible for lung injury and its sequel but may affect other organs as olfactory and 25 gustatory dysfunction and as such, should inform the general audience, especially young 26 individuals that are the most concerned [2] . Actually, we did not state that these symptoms of autonomic impairment do not require 28 specific treatment, but we believe it must be a case by case management depending on the breathing/hyperventilation syndrome in adults Efficacy of 68 Therapies for Postural Tachycardia Syndrome: A Systematic Review and Meta-69 analysis


id: cord-252569-9rv1p3qh
author: Zanella, M.-C.
date: 2019-01-11
url: https://www.sciencedirect.com/science/article/pii/S1198743X18308127
doi: 10.1016/j.cmi.2018.12.022
title:
  High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal

abstract:
  BACKGROUND: Viral aetiologies are the most common cause of central nervous system (CNS) infections. Approximately one-half of CNS infections remain of undetermined origin. High-throughput sequencing (HTS) brought new perspectives to CNS infection investigations, allowing investigation of viral aetiologies with an unbiased approach. HTS use is still limited to specific clinical situations. OBJECTIVES: The aim of this review was to evaluate the contribution and pitfalls of HTS for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis in CNS patient samples. SOURCES: PubMed was searched from 1 January 2008 to 2 August 2018 to retrieve available studies on the topic. Additional publications were included from a review of full-text sources. CONTENT: Among 366 studies retrieved, 29 used HTS as a diagnostic technique. HTS was performed in cerebrospinal fluid and brain biopsy samples of 307 patients, including immunocompromised, immunocompetent paediatric, and adult cases. HTS was performed retrospectively in 18 studies and prospectively in 11. HTS led to the identification of a potential causal virus in 41 patients, with 11 viruses known and ten not expected to cause CNS infections. Various HTS protocols were used. IMPLICATIONS: The additional value of HTS is difficult to quantify because of various biases. Nevertheless, HTS led to the identification of a viral cause in 13% of encephalitis, meningoencephalitis, and meningitis cases in which various assays failed to identify the cause. HTS should be considered early in clinical management as a complement to routine assays. Standardized strategies and systematic studies are needed for the integration of HTS in clinical management.


id: cord-253250-zet48zcl
author: Thaden, J.T.
date: 2020-09-09
url: https://www.sciencedirect.com/science/article/pii/S1198743X20305292?v=s5
doi: 10.1016/j.cmi.2020.09.002
abstract: nan
title:
  When two for the price of one isn’t a bargain: Estimating prevalence and microbiology of bacterial co-infections in patients with COVID-19


id: cord-256402-b5fel2d3
title: Safety considerations of chloroquine and hydroxychloroquine in treatment of COVID-19
author: Gevers, S.
date: 2020-05-16
url: https://www.ncbi.nlm.nih.gov/pubmed/32422406/
doi: 10.1016/j.cmi.2020.05.006
abstract:
  Chloroquine and hydroxychloroquine are both used to treat COVID-19. Safety data in this specific population is largely unknown. In particular, cardiologic, gastro-intestinal and neuropsychiatric side-effects of (hydroxychloroquine) needs special attention in COVID-19 patients.


id: cord-257248-aii0tj9x
author: O'Grady, K.F.
date: 2016-02-22
url: https://api.elsevier.com/content/article/pii/S1198743X16001129
doi: 10.1016/j.cmi.2016.02.004
title:
  Prevalence, codetection and seasonal distribution of upper airway viruses and bacteria in children with acute respiratory illnesses with cough as a symptom

abstract:
  Most studies exploring the role of upper airway viruses and bacteria in paediatric acute respiratory infections (ARI) focus on specific clinical diagnoses and/or do not account for virus–bacteria interactions. We aimed to describe the frequency and predictors of virus and bacteria codetection in children with ARI and cough, irrespective of clinical diagnosis. Bilateral nasal swabs, demographic, clinical and risk factor data were collected at enrollment in children aged <15 years presenting to an emergency department with an ARI and where cough was a symptom. Swabs were tested by polymerase chain reaction for 17 respiratory viruses and seven respiratory bacteria. Logistic regression was used to investigate associations between child characteristics and codetection of the organisms of interest. Between December 2011 and August 2014, swabs were collected from 817 (93.3%) of 876 enrolled children, median age 27.7 months (interquartile range 13.9–60.3 months). Overall, 740 (90.6%) of 817 specimens were positive for any organism. Both viruses and bacteria were detected in 423 specimens (51.8%). Factors associated with codetection were age (adjusted odds ratio (aOR) for age <12 months = 4.9, 95% confidence interval (CI) 3.0, 7.9; age 12 to <24 months = 6.0, 95% CI 3.7, 9.8; age 24 to <60 months = 2.4, 95% CI 1.5, 3.9), male gender (aOR 1.46; 95% CI 1.1, 2.0), child care attendance (aOR 2.0; 95% CI 1.4, 2.8) and winter enrollment (aOR 2.0; 95% CI 1.3, 3.0). Haemophilus influenzae dominated the virus–bacteria pairs. Virus–H. influenzae interactions in ARI should be investigated further, especially as the contribution of nontypeable H. influenzae to acute and chronic respiratory diseases is being increasingly recognized.


id: cord-257696-ybu772zw
author: Bartoletti, Michele
date: 2020-09-22
url: https://api.elsevier.com/content/article/pii/S1198743X20305632
doi: 10.1016/j.cmi.2020.09.014
title:
  Efficacy of corticosteroid treatment for hospitalized patients with severe COVID-19: a multicenter study

abstract:
  OBJECTIVES: To assess the efficacy of corticosteroids in patients with coronavirus disease 2019 (COVID-19) METHODS: Multicenter observational study from February 22 through June 30, 2020. We included consecutive adult patients with severe COVID-19 defined as respiratory rate ≥30 breath per minute, oxygen saturation ≤93% on ambient air or arterial partial pressure of oxygen to fraction of inspired oxygen ≤300 mmHg. We excluded patients treated with other immunomodulant drugs, receiving low dose of corticosteroids and those receiving corticosteroids after 72h from admission. The primary endpoint was 30-day mortality form hospital admission. The main exposure variable was corticosteroid therapy at dosage of ≥0.5 mg/kg of prednisone equivalents. It was introduced as binomial covariate in a logistic regression model for primary endpoint and inverse probability of treatment weighting using the propensity score. RESULTS: Of 1717 patients with COVID-19 evaluated, 513 patients were included in the study; of these 170 (33%) were treated with corticosteroids. During the hospitalization 166 (34%) patients reached the primary outcome [60/170 (35%) in the corticosteroid group and 106/343 (31%) in the non-corticosteroid group]. At multivariable analysis corticosteroid treatment was not associated with lower 30-day mortality rate [aOR 0.59 (0.20-1.74), p=0.33]. After inverse probability of treatment weighting, corticosteroids were not associated to lower 30-day mortality [average treatment effect 0.05 (95% -0.02 to 0.09), p=0.12]. However, subgroup analysis revealed that in patients with PO(2)/FiO(2) < 200 mmHg at admission [135 patients, 52 (38%) treated with corticosteroids] corticosteroid treatment was associated to a lower risk of 30-day mortality [23/52 (44%) vs 45/83 (54%), aOR 0.20 (95%CI 0.04 to 0.90), p=0.036]. CONCLUSION: Our study shows that the effect of corticosteroid treatment on mortality might be limited to critically ill COVID-19 patients.


id: cord-264261-98h1bmb2
title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results
author: Caruana, Giorgia
date: 2020-06-25
url: https://www.ncbi.nlm.nih.gov/pubmed/32593741/
doi: 10.1016/j.cmi.2020.06.019
abstract:
  BACKGROUND: To face the current COVID-19 pandemic, diagnostic tools are essential. It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. Further studies are warranted to define the role of serological diagnosis and a possible correlation between serological response and prognosis. OBJECTIVES: To guide clinical microbiologists in the use of these diagnostic tests and clinicians in the interpretation of their results. SOURCES: A research of literature was performed through PubMed and Google Scholar using the keywords SARS-CoV-2, SARS-CoV-2 molecular diagnosis, SARS-CoV-2 immune response, SARS-CoV-2 serology/antibody testing, coronavirus diagnosis. CONTENT: The present review discusses performances, limitations and use of current and future diagnostic tests for SARS-CoV-2. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes.


id: cord-265363-xw56intn
author: Gautret, P.
date: 2014-12-12
url: https://doi.org/10.1111/j.1469-0691.2009.02816.x
doi: 10.1111/j.1469-0691.2009.02816.x
title:
  Incidence of Hajj-associated febrile cough episodes among French pilgrims: a prospective cohort study on the influence of statin use and risk factors

abstract:
  A prospective epidemiological study was conducted to evaluate the incidence of febrile cough episodes among adult Muslims travelling from Marseille to Saudi Arabia during the Hajj pilgrimage and to assess if use of statin had an influence on this incidence. In total, 580 individuals were presented with a questionnaire. A significant proportion of individuals had chronic medical disorders, e.g. diabetes mellitus (132, 22.8%) and hypertension (147, 25.3%). Pilgrims had a low level of education and a low employment rate. Sixty (10.3%) were treated with statins for hypercholesterolemia. Four hundred and fourty-seven pilgrims were presented a questionnaire on returning home. A total of 74 travellers (16.6%) experienced fever during their stay in Saudi Arabia (67 attended a doctor) and 271 (60.6%) had cough (259 attended a doctor); 70 travellers with cough were febrile (25.9%). Seventy per cent of the travellers who suffered cough episodes developed their first symptoms within 3 days, suggesting a human to human transmission of the responsible pathogen, with short incubation time as evidenced by a bimodal distribution of cough in two peaks at a 24 h interval. None of demographical and socioeconomic characteristics, underlying diseases or vaccination against influenza significantly affected the occurrence of cough. Diabetes correlated with an increased risk of febrile cough (OR = 2.02 (1.05–3.89)) as well as unemployment (OR = 2.22 (0.91–5.53)). Use of statins had no significant influence on the occurrence of cough and/or fever during the pilgrimage. This result suggests that while treatment with a statin has been demonstrated to reduce the mortality from severe sepsis associated with respiratory tract infections, it probably does not play a role in the outcome of regular febrile cough episodes as observed in the cohort studied here.


id: cord-270947-6e5cw2q9
author: Huang, H.-S.
date: 2017-12-05
url: https://www.ncbi.nlm.nih.gov/pubmed/29208560/
doi: 10.1016/j.cmi.2017.11.018
title:
  Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis

abstract:
  OBJECTIVES: To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)—BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays—on the detection of viral respiratory infections. METHODS: A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay. RESULTS: Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848–0.949), 0.949 (95% confidence interval, 0.882–0.979) and 0.954 (95% confidence interval, 0.871–0.985), respectively. The three mPCRs were comparable in terms of detection of FluA. CONCLUSIONS: Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.


id: cord-275068-yr076sl6
title: Football and COVID-19 risk: correlation is not causation
author: Ayoub, Fares
date: 2020-09-03
txt: ./txt/cord-275068-yr076sl6.txt
cache: ./cache/cord-275068-yr076sl6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.cmi.2020.08.034
doi: 10.1016/j.cmi.2020.08.034
abstract: nan
summary:
  A recent 8 genome wide association analysis (GWAS) has implicated that blood group A patients had a higher risk 9 of severe COVID-19 compared to other blood types,[3] while other studies have found associations 10 between vitamin D levels/latitude, and Bacille de Calmette et Guérin (BCG) vaccine and mortality to 11 COVID-19. [4] Based on the results of these studies, shall we tell our blood group A patients to stay home 12 or tell everyone to take vitamin D or get vaccinated with BCG? [5] Low vitamin D levels have often been associated with a 16 higher risk of infections, but vitamin D supplementation has not been shown to prevent respiratory 17 1 impact journals during the pandemic, but it is important to remember that correlation does not equal 2 causation.


id: cord-275556-798oed8n
author: Piubelli, Chiara
date: 2020-10-12
txt: ./txt/cord-275556-798oed8n.txt
cache: ./cache/cord-275556-798oed8n.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.cmi.2020.10.006
doi: 10.1016/j.cmi.2020.10.006
summary:
  OBJECTIVES: In Italy the burden of patients with Coronavirus Disease 2019 (Covid-19) gradually decreased from March to the end of May. In this work, we aimed at evaluating a possible association between the severity of clinical manifestations and viral load over time, during the epidemiological transition from high to low transmission setting. CONCLUSIONS: We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive care, along with decreasing median values of viral load. The proportion of patients requiring intensive care significantly reduced from 6.7% ( We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive 46 care, along with decreasing median values of viral load. As the epidemiological context changes 47 from high to low transmission setting, people are presumably exposed to a lower viral load, which 48 has been previously associated to less severe clinical manifestations.

title:
  Overall decrease of SARS-CoV-2 viral load and reduction of clinical burden: the experience of a Northern Italy hospital

abstract:
  OBJECTIVES: In Italy the burden of patients with Coronavirus Disease 2019 (Covid-19) gradually decreased from March to the end of May. In this work, we aimed at evaluating a possible association between the severity of clinical manifestations and viral load over time, during the epidemiological transition from high to low transmission setting. METHODS: We reviewed the cases of Covid-19 diagnosed at the Emergency Room of our hospital, retrieving the proportion of patients admitted to the intensive care unit. A raw estimation of the viral load was done evaluating the Ct (cycle threshold) trend obtained from our diagnostic Reverse Transcriptase real-time PCR test. RESULTS: The proportion of patients requiring intensive care significantly reduced from 6.7% (19/281) in March, to 1.1% (1/86) in April, and to none in May (Fisher’s test p-value=0.0067). As for viral load, we observed a trend of Ct increasing from a median value of 24 (IQR 19-29) to 34 (IQR 29-37) between March and May, with a statistically significant difference between March and April (Pairwise Wilcoxon test with Stepdown Bonferroni Adjustment for multiple testing, p=0.0003). CONCLUSIONS: We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive care, along with decreasing median values of viral load. As the epidemiological context changes from high to low transmission setting, people are presumably exposed to a lower viral load, which has been previously associated to less severe clinical manifestations.


id: cord-276212-ys5njiw0
author: Wei, L.
date: 2015-05-30
url: https://www.ncbi.nlm.nih.gov/pubmed/26033670/
doi: 10.1016/j.cmi.2015.05.027
title:
  Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong

abstract:
  Respiratory viruses cause acute respiratory diseases with a broad and overlapping spectrum of symptoms. We examined the clinical symptoms and explored the patterns of various respiratory viral infections in children in Hong Kong. Among 2090 specimens collected from outpatient care (2007–2010), 1343 (64.3%) were positive for any virus by the xTAG assay, and 81 (3.9%) were positive for co-infection. The most frequently detected viruses among children aged 6–15 years were enterovirus/rhinovirus and influenza virus A, whereas most non-influenza viruses were more frequently detected in younger children. Higher body temperature was more common for illnesses associated with influenza viruses than for those associated with non-influenza viruses, but other symptoms were largely similar across all infections. The seasonality pattern varied among different viruses, with influenza virus A being the predominant virus detected in winter, and enterovirus/rhinovirus being more commonly detected than influenza virus A in the other three seasons, except for 2009.


id: cord-276399-omjfyog0
author: To, K.K.W.
date: 2019-04-18
url: https://doi.org/10.1016/j.cmi.2019.04.012
doi: 10.1016/j.cmi.2019.04.012
title:
  Respiratory virus infection among hospitalized adult patients with or without clinically apparent respiratory infection: a prospective cohort study

abstract:
  OBJECTIVES: To determine the viral epidemiology and clinical characteristics of patients with and without clinically apparent respiratory tract infection. METHODS: This prospective cohort study was conducted during the 2018 winter influenza season. Adult patients with fever/respiratory symptoms (fever/RS group) were age- and sex-matched with patients without fever/RS (non-fever/RS group) in a 1:1 ratio. Respiratory viruses were tested using NxTAG™ Respiratory Pathogen Panel IVD, a commercially-available multiplex PCR panel. RESULTS: A total of 214 acutely hospitalized patients were included in the final analysis, consisting of 107 with fever/RS (fever/RS group), and 107 age- and sex-matched patients without fever/RS (non-fever/RS group). Respiratory viruses were detected in 34.1% (73/214) of patients, and co-infection occurred in 7.9% (17/214) of patients. The incidence of respiratory virus was higher in the fever/RS group than in the non-fever/RS group (44.9% (48/107) versus 23.4% (25/107), p 0.001). Influenza B virus, enterovirus/rhinovirus and coronaviruses were detected more frequently in the fever/RS group, whereas parainfluenza virus 4B and adenovirus were detected more frequently in the non-fever/RS group. Among the non-fever/RS group, chest discomfort was more common among patients tested positive for respiratory viruses than those without respiratory virus detected (44% (11/25) versus 22% (18/82), p 0.04). CONCLUSIONS: Respiratory viruses can be frequently detected among hospitalized patients without typical features of respiratory tract infection. These patients may be a source of nosocomial outbreaks.


id: cord-278807-p1crrb8n
author: Antón, A.
date: 2016-03-02
url: https://api.elsevier.com/content/article/pii/S1198743X16001154
doi: 10.1016/j.cmi.2016.02.007
title:
  Virological surveillance of influenza and other respiratory viruses during six consecutive seasons from 2006 to 2012 in Catalonia, Spain

abstract:
  Most attention is given to seasonal influenza and respiratory syncytial virus outbreaks, but the cumulative burden caused by other respiratory viruses (RV) is not widely considered. The aim of the present study is to describe the circulation of RV in the general population during six consecutive seasons from 2006 to 2012 in Catalonia, Spain. Cell culture, immunofluorescence and PCR-based assays were used for the RV laboratory-confirmation and influenza subtyping. Phylogenetic and molecular characterizations of viral haemagglutinin, partial neuraminidase and matrix 2 proteins were performed from a representative sampling of influenza viruses. A total of 6315 nasopharyngeal samples were collected, of which 64% were laboratory-confirmed, mainly as influenza A viruses and rhinoviruses. Results show the significant burden of viral aetiological agents in acute respiratory infection, particularly in the youngest cases. The study of influenza strains reveals their continuous evolution through either progressive mutations or by segment reassortments. Moreover, the predominant influenza B lineage was different from that included in the recommended vaccine in half of the studied seasons, supporting the formulation and use of a quadrivalent influenza vaccine. Regarding neuraminidase inhibitors resistance, with the exception of the 2007/08 H275Y seasonal A(H1N1) strains, no other circulating influenza strains carrying known resistance genetic markers were found. Moreover, all circulating A(H1N1)pdm09 and A(H3N2) strains finally became genetically resistant to adamantanes. A wide knowledge of the seasonality patterns of the RV in the general population is well-appreciated, but it is a challenge due to the unpredictable circulation of RV, highlighting the value of local and global RV surveillance.


id: cord-279111-jaa45kyc
author: Ieven, M.
date: 2018-02-12
url: https://api.elsevier.com/content/article/pii/S1198743X18301526
doi: 10.1016/j.cmi.2018.02.004
title:
  Aetiology of lower respiratory tract infection in adults in primary care: a prospective study in 11 European countries

abstract:
  OBJECTIVES: To describe the role of bacteria (including bacterial resistance), viruses (including those recently described) and mixed bacterial–viral infections in adults presenting to primary care with lower respiratory tract infection (LRTI). METHODS: In all, 3104 adults with LRTI were enrolled, of whom 141 (4.5%) had community-acquired pneumonia (CAP), and 2985 matched controls in a prospective study in 16 primary care networks in Europe, and followed patients up at 28–35 days. We detected Streptococcus pneumoniae and Haemophilus influenzae and assessed susceptibility, atypical bacteria and viruses. RESULTS: A potential pathogen was detected in 1844 (59%) (in 350 (11%) bacterial pathogens only, in 1190 (38%) viral pathogens only, and in 304 (10%) both bacterial and viral pathogens). The most common bacterial pathogens isolated were S. pneumoniae (5.5% overall, 9.2% in CAP patients) and H. influenzae (5.4% overall, 14.2% in CAP patients). Less than 1% of S. pneumoniae were highly resistant to penicillin and 12.6% of H. influenzae were β-lactamase positive. The most common viral pathogens detected were human rhinovirus (20.1%), influenza viruses (9.9%), and human coronavirus (7.4%). Influenza virus, human parainfluenza viruses and human respiratory syncytial virus as well as human rhinovirus, human coronavirus and human metapneumovirus were detected significantly more frequently in LRTI patients than in controls. CONCLUSIONS: A bacterial pathogen is identified in approximately one in five adult patients with LRTI in primary care, and a viral pathogen in just under half, with mixed infections in one in ten. Penicillin-resistant pneumococci and β-lactamase-producing H. influenzae are uncommon. These new findings support a restrictive approach to antibiotic prescribing for LRTI and the use of first-line, narrow-spectrum agents in primary care.


id: cord-279125-w6sh7xpn
title: Digital microbiology
author: Egli, Adrian
date: 2020-06-27
url: https://api.elsevier.com/content/article/pii/S1198743X20303670
doi: 10.1016/j.cmi.2020.06.023
abstract:
  BACKGROUND: Digitalisation and artificial intelligence have an important impact on the way microbiology laboratories will work in the near future. Opportunities and challenges lay ahead to digitalise the microbiological workflows. Making an efficient use of big data, machine learning, and artificial intelligence in clinical microbiology requires a profound understanding of data handling aspects. OBJECTIVE: This review article summarizes the most important concepts of digital microbiology. The article provides microbiologists, clinicians and data scientists a viewpoint and practical examples along the diagnostic process. SOURCES: We used peer-reviewed literature identified by a Pubmed search for digitalisation, machine learning, artificial intelligence and microbiology. CONTENT: We describe the opportunities and challenges of digitalisation in microbiological diagnostic process with various examples. We also provide in this context key aspects of data structure and interoperability, as well as legal aspects. Finally, we outline the way for applications in a modern microbiology laboratory. IMPLICATIONS: We predict that digitalization and the usage of machine learning will have a profound impact on the daily routine of the laboratory staff. Along the analytical process, the most important steps should be identified, where digital technologies can be applied and provide a benefit. The education of all staff involved should be adapted to prepare for the advances in digital microbiology.


id: cord-283411-40ojqv1y
author: Ben-Shmuel, Amir
date: 2020-09-10
txt: ./txt/cord-283411-40ojqv1y.txt
cache: ./cache/cord-283411-40ojqv1y.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1198743X20305322?v=s5
doi: 10.1016/j.cmi.2020.09.004
summary:
  title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit.

title:
  Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities

abstract:
  OBJECTIVES: Environmental surfaces have been suggested as likely contributors to the transmission of COVID-19. This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. METHODS: SARS-CoV-2 virus stability and infectivity on non-porous surfaces was tested under controlled laboratory conditions. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected by RT-PCR and infectivity was assessed by VERO E6 CPE test. RESULTS: In laboratory-controlled conditions, SARS-CoV-2 gradually lost its infectivity completely at day 4 at ambient temperature and the decay rate of viral viability on surfaces directly correlated with increase in temperature. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. None of the surface and air samples from all three sites (0/97) were found to contain infectious titers SARS-Cov-2 in tissue culture assay. CONCLUSIONS: Despite prolonged viability of SARS-CoV-2 in laboratory-controlled conditions, uncultivable viral contamination on inanimate surfaces might suggest low feasibility for indirect fomite transmission.


id: cord-283818-4m9p717r
author: Yan, Chao
date: 2020-04-08
url: https://www.ncbi.nlm.nih.gov/pubmed/32276116/
doi: 10.1016/j.cmi.2020.04.001
title:
  Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay

abstract:
  OBJECTIVE: To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase chain reaction (RT-PCR). METHODS: We designed primers specific to the orf1ab and S genes of SARS-CoV-2. Total viral RNA was extracted using the QIAamp Viral RNA Mini Kit. We optimized the RT-LAMP assay. And, this assay was evaluated for its sensitivity and specificity of detection using real-time turbidity monitoring and visual observation. RESULTS: The primer sets orf1ab-4 and S-123 amplified the genes in the shortest times, the mean (±SD) time was 18 ± 1.32 min and 20 ± 1.80 min, respectively, and 63°C was the optimum reaction temperature. The sensitivity was 2×10(1) copies and 2×10(2) copies per reaction with primer sets orf1ab-4 and S-123, respectively. This assay showed no cross-reactivity with other 60 respiratory pathogens. To describe the availability of this method in clinical diagnosis, we collected 130 specimens from patients with clinically suspected SARS-CoV-2 infection. Among them, 58 were confirmed to be positive and 72 were negative by RT-LAMP. The sensiticity was 100% (95% CI 92.3% - 100%), specificity 100% (95% CI 93.7% - 100%). This assay detected SARS-CoV-2 in the mean (±SD) time of 26.28 ± 4.48 min and the results can be identified with visual observation. CONCLUSION: These results demonstrate that we developed a rapid, simple, specific, and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. It will be a powerful tool for SARS-CoV-2 identification, and for monitoring suspected patients, close contacts, and high-risk groups.


id: cord-286544-ipmcqz8n
title: Predictors of progression from moderate to severe COVID-19: a retrospective cohort
author: Cheng, Biao
date: 2020-07-02
url: https://www.ncbi.nlm.nih.gov/pubmed/32622952/
doi: 10.1016/j.cmi.2020.06.033
abstract:
  OBJECTIVE: Most coronavirus disease 2019 (COVID-19) cases were identified as moderate, which is defined as having a fever or dry cough and lung imaging with ground-glass opacities. The risk factors and predictors of prognosis in such cohorts remain uncertain. METHODS: All adult patients with COVID-19 of moderate severity diagnosed using qRT-PCR and hospitalized at the Central Hospital of Wuhan, China, from Jan 1 to Mar 20, 2020 were enrolled in this retrospective study. The main outcomes were progression from moderate to severe or critical condition or death. RESULTS: Among the 456 enrolled patients with moderate COVID-19, 251/456 (55.0%) had poor prognosis. Multivariate logistic regression analysis identified higher NLR on admission (OR =1.032, 95%CI 1.042-1.230, P = 0.004) and higher CRP on admission (OR =3.017, 95%CI 1.941-4.690, P < 0.001) were associated with increased odds ratios of poor prognosis. The area under the receiver operating characteristic (ROC) curve (AUC) for NLR and CRP in predicting progression to critical condition was 0.77 (95% CI 0.694-0.846, P < 0.001) and 0.84 (95% CI 0.780-0.905, P < 0.001), with a cut-off value of 2.79 and 25.95 mg/l, respectively. The AUC of NLR and CRP in predicting death was 0.81 (95% CI, 0.732-0.878, P < 0.001) and 0.89 (95% CI 0.825-0.946, P < 0.001), with a cut-off value of 3.19 and 33.4 mg/l, respectively. CONCLUSIONS: Higher levels of NLR and CRP at admission were associated with poor prognosis of moderate COVID-19 patients. NLR and CRP were good predictors of progression to critical condition and death.


id: cord-287256-hgqz1bcs
author: Magurano, Fabio
date: 2020-11-05
url: https://www.sciencedirect.com/science/article/pii/S1198743X20306881?v=s5
doi: 10.1016/j.cmi.2020.10.034
title:
  SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature

abstract:
  Objectives The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Methods The virus was inoculated on plastic surface and harvested at predefined time-points in parallel at 20-25°C (RT) and at 28°C (JT). Samples collections were tested by TCID50 titers on Vero cells. Samples collections were tested by TCID50 titers on Vero cells. Results Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID50 viral titre of 0,67 and 0,25 log10 respectively. At RT, an important reduction in the viral titre, from 4 log10 to 3 log10 TCID50 was observed during the first 24-36 hours. At JT the same decay was observed more rapidly (between 8 and 12 hours), The rate of viral inactivation by D-value was 24.74 at RT and 12,21 hours at JT. Conclusions This remarkable difference between the two temperatures suggests that virus vitality can be influenced by the environmental temperature and that the hot season could reduce the probability of COVID-19 transmission.


id: cord-288425-po35m6d9
author: Albert, Eliseo
date: 2020-11-13
txt: ./txt/cord-288425-po35m6d9.txt
cache: ./cache/cord-288425-po35m6d9.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1198743X20306972?v=s5
doi: 10.1016/j.cmi.2020.11.004
summary:
  We 25 evaluated the Panbio™ COVID-19 Ag Rapid Test Device for COVID-19 diagnosis in 26 symptomatic patients (n=412) attended in primary healthcare centers. Sensitivity of SARS-CoV-2 RAD 135 assays has been reported to vary between 45%-97% [3-7], yet direct comparison 136 between studies is hampered by marked dissimilarities in patient clinical characteristics 137 and age, testing sites, type of specimen processed, and time to testing, among others. In line with 146 previous reports [2-4], SARS-CoV-2 RNA load was significantly higher in RT-PCR+/ 147 RAD+ specimens than in RT-PCR+/ RAD-samples. In our setting, specimens with RT-148 PCR C T >25 (equivalent to SARS-CoV-2 RNA loads < 5.9 log 10 copies/ml) returned 149 discordant RAD/RT-PCR results. An important observation of our study was that SARS-CoV-2 could not be cultured 151 from RT-PCR+ (C T >25)/RAD-specimens. Antigen-based testing but not real-time PCR correlates with SARS-CoV-2 virus 198 culture Evaluation of 216 rapid antigen test for detection of SARS-CoV-2 virus

title:
  Field evaluation of a rapid antigen test (Panbio™ COVID-19 Ag Rapid Test Device) for COVID-19 diagnosis in primary healthcare centers

abstract:
  OBJECTIVES: To our knowledge no previous study has assessed the performance of a rapid antigen diagnostic immunoassay (RAD) conducted at the point of care (POC). We evaluated the Panbio™ COVID-19 Ag Rapid Test Device for COVID-19 diagnosis in symptomatic patients (n=412) attended in primary healthcare centers. METHODS: RAD was performed immediately after sampling following the manufacturer’s instructions (reading at 15 min.). RT-PCRs were carried out within 24 h. of specimen collection. Samples displaying discordant results were processed for culture in Vero E6 cells. Presence of SARS-CoV-2 in cell cultures was confirmed by RT-PCR. RESULTS: Out of 412 patients, 43 (10.4%) tested positive by RT-PCR and RAD and 358 (86.9%) negative by both methods, showing discordant results (RT-PCR+/RAD-) in 11 patients (2.7%). Overall specificity and sensitivity of rapid antigen detection (RAD) was 100% (95% CI, 98.7-100%), and 79.6% (95% CI, 67.-88.8%), respectively, taking RT-PCR as the reference. Overall RAD negative predictive value for an estimated prevalence of 5% and 10% was 99% (95% CI, 97.4-99.6%) and 97.9% (95% CI, 95.9-98.9), respectively. SARS-CoV-2 could not be cultured from specimens yielding RT-PCR+/RAD-results (n=11). CONCLUSION: The Panbio™ COVID-19 Ag Rapid Test Device performed well as a POCT for early diagnosis of COVID-19 in primary healthcare centers. More crucially, the data suggested that patients with RT-PCR-proven COVID-19 testing negative by RAD are unlikely to be infectious.


id: cord-291272-srt08jh8
author: Peters, E.J.G.
date: 2020-10-14
url: https://www.sciencedirect.com/science/article/pii/S1198743X20306157?v=s5
doi: 10.1016/j.cmi.2020.10.004
title:
  Outcomes of persons with COVID-19 in hospitals with and without standard treatment with (Hydroxy)chloroquine

abstract:
  OBJECTIVE: To compare survival of subjects with COVID-19 treated in hospitals that either did or did not routinely treat patients with hydroxychloroquine or chloroquine. METHODS: We analysed data of COVID-19 patients treated in 9 hospitals in the Netherlands. Inclusion dates ranged from February 27(th) 2020, to May 15(th), when the Dutch national guidelines no longer supported the use of (hydroxy)chloroquine. Seven hospitals routinely treated subjects with (hydroxy)chloroquine, two hospitals did not. Primary outcome was 21-day all-cause mortality. We performed a survival analysis using log-rank test and Cox-regression with adjustment for age, sex and covariates based on premorbid health, disease severity, and the use of steroids for adult respiratory distress syndrome, including dexamethasone. RESULTS: Among 1949 included subjects, 21-day mortality was 21.5% in 1596 subjects treated in hospitals that routinely prescribed (hydroxy)chloroquine, and 15.0% in 353 subjects that were treated in hospitals that did not. In the adjusted Cox-regression models this difference disappeared, with an adjusted hazard ratio of 1.09 (95%CI 0.81-1.47). When stratified by actually received treatment in individual subjects, the use of (hydroxy)chloroquine was associated with an increased 21-day mortality (HR 1.58; 95%CI 1.24-2.02) in the full model. CONCLUSIONS: After adjustment for confounders, mortality was not significantly different in hospitals that routinely treated patients with (hydroxy)chloroquine, compared with hospitals that did not. We compared outcomes of hospital strategies rather than outcomes of individual patients to reduce the chance of indication bias. This study adds evidence against the use of (hydroxy)chloroquine in hospitalised patients with COVID-19.


id: cord-291729-4l4v9jxd
title: Sample pooling for SARS-COV-2 RT-PCR screening
author: de Salazar, Adolfo
date: 2020-09-10
url: https://api.elsevier.com/content/article/pii/S1198743X20305371
doi: 10.1016/j.cmi.2020.09.008
abstract:
  OBJECTIVE: To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of COVID-19, by using different commercial platforms for nucleic acid extraction and amplification. METHODS: 3519 nasopharyngeal samples received at 9 Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of 10 samples and 11 pools of 9 samples) according to the existing methodology in each of the centres. RESULTS: We found that 253 pools (2519 samples) were negative, and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples) we found discordant results when compared to their correspondent individual samples: in 22/29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity, positive and negative predictive values for pooling were 97.10% (CI95%; 94.11-98.82), 100%, 100% and 99.79% (CI95%; 99.56-99.90) respectively; accuracy was 99.80% (CI95%; 99.59-99.92) and kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted into a median loss of 2.87 (CI95%; 2.46-3.28) CTs for E gene, 3.36 (CI95%; 2.89-3.85) CTs for RdRP gene and 2.99 (CI95%; 2.56-3.43) CTs for N gene. CONCLUSION: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values.


id: cord-293542-o0zspgrk
title: Facing the threat of highly infectious diseases in Europe: the need for a networking approach
author: Ippolito, G.
date: 2014-12-12
url: https://www.ncbi.nlm.nih.gov/pubmed/19486072/
doi: 10.1111/j.1469-0691.2009.02876.x
abstract:
  In recent years emerging and re-emerging infections, as well as the risk of bioterrorist events, have attracted increasing attention from health authorities because of the epidemic potential that renders some of them a real public health challenge. These highly infectious diseases (HIDs) are occurring more and more frequently in Europe, and despite the many initiatives in place to face them, many unsolved problems remain, and coordinated efforts for dealing with HIDs appear mandatory. Whereas uncoordinated measures would lead to only partial and poor responses to these emerging threats, networking represents a valuable approach to these diseases, in order to: (i) ensure a rapid and effective response; (ii) stimulate complementarity and prevent duplication; (iii) promote international cooperation, exchange of experience, good practice and protocols; and (iv) support the less prepared countries in the European Community.


id: cord-294392-a8s66g96
author: Zhang, Shuai
date: 2020-09-07
url: https://www.sciencedirect.com/science/article/pii/S1198743X20305218?v=s5
doi: 10.1016/j.cmi.2020.08.038
title:
  Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study

abstract:
  OBJECTIVES: We aim to describe the fraction of asymptomatic health-care workers (HCWs) in two designated hospitals for COVID-19 treatment in Wuhan and explore the factors associated with asymptomatic SARS-CoV-2 infection. METHODS: All HCWs in Wuhan Union Hospital and Wuhan Red Cross Hospital with either positive SARS-CoV-2 nucleic acid or antibody test before April 18, 2020 were included. Exposure, epidemiologic, demographic information were retrospectively collected by a structured questionnaire. Medical records were also reviewed for clinical characteristics and CT images in HCWs. RESULTS: As of April 18, 2020, a total of 424 HCWs were identified. Among them, 276 (65.1%) were symptomatic and 148 (34.9%) were asymptomatic. 55 (19.9%) families of the symptomatic HCWs and 16 (10.8%) families of the asymptomatic HCWs were infected with SARS-CoV-2. HCWs with infected family members tend to be symptomatic cases (Odds ratio [OR], 2.053 [95% confidence interval (CI), 1.130-3.730]; P=0.018). Multivariable logistic regression analysis exhibited that performing tracheal intubation or extubation (OR, 4.057 [95% CI, 1.183-13.909]; P=0.026) was associated with an increased likelihood of symptomatic SARS-CoV-2 infection, while consistent use of N95 respirators (OR, 0.369 [95% CI, 0.201-0.680]; P=0.001) and eye protection (OR, 0.217 [95% CI, 0.116-0.404]; P<0.001) were associated with an increased likelihood of asymptomatic SARS-CoV-2 infection. CONCLUSIONS: Asymptomatic SARS-CoV-2 infection in HCWs occupies a considerable proportion during the pandemic of COVID-19. Those who have performed tracheal intubation or extubation were most likely to develop related symptoms, while those taking aggressive measures including consistent use of N95 masks, and eye protection tended to be asymptomatic cases.


id: cord-294546-0otd1heg
author: Prendki, V.
date: 2019-01-12
url: https://doi.org/10.1016/j.cmi.2018.12.037
doi: 10.1016/j.cmi.2018.12.037
title:
  Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

abstract:
  OBJECTIVES: We aimed to assess the accuracy of PCR detection of viruses and bacteria on nasopharyngeal and oropharyngeal swabs (NPS) for the diagnosis of pneumonia in elderly individuals. METHODS: We included consecutive hospitalized elderly individuals suspected of having pneumonia. At inclusion, NPS were collected from all participants and tested by PCR for the presence of viral and bacterial respiratory pathogens (index test, defined as comprehensive molecular testing). Routine diagnostic tests (blood and sputum culture, urine antigen detection) were also performed. The reference standard was the presence of pneumonia on a low-dose CT scan as assessed by two independent expert radiologists. RESULTS: The diagnosis of pneumonia was confirmed in 127 of 199 (64%) included patients (mean age 83 years, community-acquired pneumonia in 105 (83%)). A pathogen was identified by comprehensive molecular testing in 114 patients (57%) and by routine methods in 22 (11%). Comprehensive molecular testing was positive for viruses in 62 patients (31%) and for bacteria in 73 (37%). The sensitivity and specificity were 61% (95% CI 53%–69%) and 50% (95% CI 39%–61%) for comprehensive molecular testing, and 14% (95% CI 82%–21%) and 94% (95% CI 86%–98%) for routine testing, respectively. Positive likelihood ratio was 2.55 for routine methods and 1.23 for comprehensive molecular testing. CONCLUSION: Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. Hence, comprehensive molecular testing is unlikely to impact clinical decision-making (NCT02467192). CLINICAL TRIALS REGISTRATION: NCT02467192.


id: cord-295479-mcfqs7vf
title: Post-COVID-19 chronic symptoms: a post-infectious entity?()
author: Davido, Benjamin
date: 2020-07-23
txt: ./txt/cord-295479-mcfqs7vf.txt
cache: ./cache/cord-295479-mcfqs7vf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32712242/
doi: 10.1016/j.cmi.2020.07.028
abstract: nan
summary:
  key: cord-295479-mcfqs7vf authors: Davido, Benjamin; Seang, Sophie; Tubiana, Roland; de Truchis, Pierre title: Post-COVID-19 chronic symptoms: a post-infectious entity?() date: 2020-07-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.07.028 sha: doc_id: 295479 cord_uid: mcfqs7vf nan COVID-19 : point épidémiologique du 21 mai Assistance Publique-Hôpitaux de Paris'' response to the COVID-19 88 pandemic Anosmia and Ageusia: Common Findings 90 in COVID-19 Patients Patients Recovered from COVID-19 Active Epstein-Barr virus infection in 95 post-viral fatigue syndrome serological IgG antibody response on the Abbott Architect for established SARS-CoV-99 2 infection Neurologic manifestations in hospitalized patients 102 with COVID-19: The ALBACOVID registry Cerebrovascular disease in patients with COVID-19: 106 neuroimaging, histological and clinical description Kawasaki-like multisystem inflammatory syndrome in children during the covid-19 Chikungunya-Induced Arthritis in Reunion Island: A 113 Long-Term Observational Follow-Up Study Showing Frequently Persistent Joint 114 Some Cases of Persistent Chikungunya Immunoglobulin M Positivity, and 115 No Anticyclic Citrullinated Peptide Seroconversi


id: cord-297470-lx3xwg92
author: Pan, Yunbao
date: 2020-10-07
url: https://www.ncbi.nlm.nih.gov/pubmed/33035672/
doi: 10.1016/j.cmi.2020.09.044
title:
  Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign

abstract:
  OBJECTIVES: The outbreak of 2019 coronavirus disease (COVID-19) pandemic in Wuhan, China, has subsided after a hard hit by the disease and subsequent city lockdown. Information on the number of people involved in Wuhan is still inadequate. This study aimed to describe the screening results of 61,437 community members in Wuchang District, Wuhan. METHODS: In mid-May 2020, Wuhan launched a population-scale city-wide SARS-CoV-2 testing campaign, which aimed to perform nucleic acid and viral antibody testing for citizens in Wuhan. Here we show the screening results of cluster sampled 61,437 residents in Wuchang District, Wuhan, China. RESULTS: A total of 1470 (2.39%, 95% CI: 2.27-2.52) individuals were detected positive for at least one antiviral antibody. Among the positive individuals, 324 (0.53%, 95% CI: 0.47-0.59) and 1200 (1.95%, 95% CI: 1.85-2.07) were positive for immunoglobulin IgM and IgG, respectively, and 54 (0.08%, 95% CI: 0.07-0.12) were positive for both antibodies. The positive rate of female carriers of antibodies were higher than those of male counterparts (male-to-female ratio of 0.75), especially in elderly citizens (ratio of 0.18 in 90+ age subgroup), indicating a sexual discrepancy in seroprevalence. In addition, viral nucleic acid detection using real-time PCR had showed 8 (0.013%, 95% CI: 0.006-0.026) asymptomatic virus carriers. CONCLUSIONS: The seroprevalence of SARS-CoV-2 in Wuhan was low. Most of Wuhan residents are still susceptible to this virus. Precautions, such as wearing mask, frequent hand hygiene, and proper social distance, are necessary before an effective vaccine or antiviral treatments are available.


id: cord-297625-eby014gm
title: Survival of rhinoviruses on human fingers
author: L''Huillier, A.G.
date: 2014-12-11
txt: ./txt/cord-297625-eby014gm.txt
cache: ./cache/cord-297625-eby014gm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25614158/
doi: 10.1016/j.cmi.2014.12.002
summary:
  Our study confirms that rhinovirus infectiousness is related to the viral concentration in droplets and suggests that children represent the main transmission source, which occurs only rarely via adults. We conducted a series of experiments to assess the duration of human rhinovirus infectiousness duration on fingers, as well as the impact of viral concentration on survival rates. One hour after the deposit of disrupted droplets on the fingers of the six volunteers, infectious viruses could be detected by culture in all subjects contaminated with HC droplets (6/6), in four of the six volunteers with AC droplets, and none of the six volunteers with LC droplets, which confirmed the influence of concentration on survival (Fig. 1) . Our study showed that virus survival, and therefore infectiousness, was related to the viral concentration in droplets. Potential role of hands in the spread of respiratory viral infections: studies with human parainfluenza virus 3 and rhinovirus 14

abstract:
  Rhinovirus is the main cause of the common cold, which remains the most frequent infection worldwide among humans. Knowledge and understanding of the rhinovirus transmission route is important to reduce morbidity as only preventive measures are effective. In this study, we investigated the potential of rhinovirus to survive on fingers. Rhinovirus-B14 was deposited on fingers for 30, 60, 90 and 120 min. Survival was defined as the ability of the virus to grow after 7 days, confirmed by immunofluorescence. Rhinovirus survival was not dependent on incubation time on fingers. Droplet disruption had no influence on survival. Survival was frequent with high rhinovirus concentrations, but rare with low-concentration droplets, which corresponded to the usual rhinovirus concentrations in mucus observed in children and adults, respectively. Our study confirms that rhinovirus infectiousness is related to the viral concentration in droplets and suggests that children represent the main transmission source, which occurs only rarely via adults. It confirms also that rhinovirus hand-related transmission is possible and supports hand hygiene as a key prevention measure.


id: cord-298441-77w86l8q
author: Lombardi, Andrea
date: 2020-06-20
txt: ./txt/cord-298441-77w86l8q.txt
cache: ./cache/cord-298441-77w86l8q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32569835/
doi: 10.1016/j.cmi.2020.06.013
summary:
  To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca'' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians).

title:
  Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy

abstract:
  OBJECTIVES: The management of healthcare workers (HCWs) exposed to confirmed cases of COVID-19 is still a matter of debate. We aimed to assess in this group the attack rate of asymptomatic carriers and the symptoms most frequently associated with the infection. METHODS: Occupational and clinical characteristics of HCWs who performed a nasopharyngeal swab for the detection of SARS-CoV-2 in a University Hospital from February 24, to March 31, 2020, were collected. For those who tested positive and for the asymptomatic positives we checked laboratory and clinical data as of May 22 to calculate the time necessary to become test-negative and to verify whether symptoms developed thereafter. Frequencies of positive tests were compared according to selected variables using multivariable logistic regression models. RESULTS: Positive tests were 139 among 1,573 HCWs (8.8%, 95% confidence interval [CI]: 7.5-10.3), with a marked difference between symptomatic (122/503, 24.2%) and asymptomatic (17/1,070, 1.6%) workers (p<0.001). Physicians were the group with the highest frequency of positive tests (61/582, 10.5%), whereas clerical workers and technicians displayed the lowest frequency (5/137, 3.6%). The likelihood of being positive increased with the number of reported symptoms and the strongest predictors were taste and smell alterations (odds ratio [OR]= 76.9) and fever (OR = 9.12). The median time from first positive test to a negative test was 27 days (95% CI: 24-30). CONCLUSIONS: A relevant number of HCWs can be infected by SARS-CoV-2 without displaying any symptom. Among symptomatic workers, the key symptoms to guide diagnosis are taste and smell alterations and fever. In median, almost four weeks are necessary to achieve negativity of nasopharyngeal swab.


id: cord-300023-2dg7njki
title: Contamination of healthcare workers'' mobile phones by epidemic viruses()
author: Pillet, S.
date: 2015-12-20
txt: ./txt/cord-300023-2dg7njki.txt
cache: ./cache/cord-300023-2dg7njki.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1198743X15010344
doi: 10.1016/j.cmi.2015.12.008
summary:
  We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. The aims of this study were (a) to evaluate the contamination of MPs by epidemic viruses including RV, NV, influenza A and B viruses, syncytial respiratory virus (RSV) and metapneumovirus (hMPV) in clinical settings, (b) to evaluate the behaviour of HCWs using their MPs in our center by using a blindly recorded questionnaire and (c) to correlate viral contamination of MPs with the behaviour of HCWs. The study took place at the University Hospital of Saint-Étienne, France, from January to March 2013, i.e. the period of circulation of epidemic viruses (influenza viruses, RSV, gastroenteritis-associated viruses) in our setting [22] (personal data).

abstract:
  Mobile phones (MPs) are potential reservoirs of nosocomial bacteria, but few data are available concerning viruses. We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. An anonymous behavioural questionnaire about MP use at hospital was administered to the HCWs of four adult and paediatric departments of a university hospital. After sampling personal (PMP) and/or professional MPs (digital enhanced cordless telephone, DECT), virus RNAs were extracted and amplified by one-step real-time reverse transcription–quantitative PCR. The molecular results were analysed in a masked manner in relation to the behavioural survey. Questionnaires from 114 HCWs (35 senior physicians, 30 residents, 32 nurses, 27 nurses' assistants) working either in adult (n = 58) or paediatric (n = 56) departments were analysed. Medical personnel used their PMP more frequently than paramedical HCWs (33/65 vs. 10/59, p <0.001). MPs were used during care more frequently in adult wards than in paediatric ones (46/58 vs. 27/56, p <0.001). Virus RNA was detected on 42/109 (38.5%) collected MPs, with RV found on 39, respiratory syncytial virus on three and metapneumovirus on one. The presence of virus RNA was significantly associated with MPs from the paediatric HCWs (p <0.001). MPs routinely used in hospital, even during care, can host virus RNA, especially RV. Promotion of frequent hand hygiene before and after MP use, along with frequent cleaning of MPs, should be encouraged.


id: cord-304710-gjb6zo81
title: Novel coronavirus: how things are in Wuhan
author: Khan, S.
date: 2020-02-11
txt: ./txt/cord-304710-gjb6zo81.txt
cache: ./cache/cord-304710-gjb6zo81.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1198743X20300847
doi: 10.1016/j.cmi.2020.02.005
abstract: nan
summary:
  There is a great risk of medical and clinical staff (and workers) becoming infected with 2019n-CoV because of their direct interaction with infected and suspected individuals. Working for long hours, disturbed daily routines including eating and sleeping schedules and fear of being infected are key factors that increase the risks of stress and anxiety for doctors and nurses, and may lead to their working less efficiently in terms of providing better treatment and care to patients. However, the increasing number of patients every day and the expected peak in the coming days [6] may cause a further shortage of medical staff and health and logistic issues for the frontline healthcare provider. China coronavirus: Wuhan medical staff being infected at much faster pace than reported as national death toll hits 26 Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China


id: cord-306083-juysx6yo
author: Choe, Young June
date: 2020-09-10
txt: ./txt/cord-306083-juysx6yo.txt
cache: ./cache/cord-306083-juysx6yo.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1198743X20305358?v=s5
doi: 10.1016/j.cmi.2020.09.006
summary:
  OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. A study conducted in children before the 9 implementation of PCV13, demonstrated significant associations between invasive 10 pneumococcal disease (IPD) and influenza viruses and respiratory syncytial virus (RSV), as well 11 as human metapneumovirus (hMPV), which was a novel observation [5] .

title:
  Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis

abstract:
  OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). METHODS: Children <18 years were eligible for inclusion if they had a respiratory infection and a positive PCR-based assay for respiratory viruses as well as a positive blood culture from 2010 to 2018 at a single referral centre in the United States regardless of their underlying medical condition or antibiotic treatment history. Monthly incidence rates of respiratory viruses and bacteraemia were analysed with a seasonal-trend decomposition procedure based on loess (STL) and cross-correlation functions using time series regression modelling. RESULTS: We identified 7,415 unique positive respiratory virus tests, including 2,278 RSV (31%), 1,825 influenza viruses (24%), 1,036 parainfluenza viruses (14%), 1,017 hMPV (14%), 677 seasonal coronaviruses (9%), and 582 adenoviruses (8%), and a total of 11,827 episodes of bacteraemia. Significant co-seasonality was found between all-cause bacteraemia and RSV (OR=1.76, 95% CI 1.50-2.06, P<0.001), influenza viruses (OR=1.38, 95% CI 1.13-1.68, P=0.002), and seasonal coronaviruses (OR=1.18, 95% CI 1.09-1.28, P<0.001), respectively. Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. Staphylococcus aureus and Streptococcus pneumoniae were the most commonly identified pathogens causing bacteraemia. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. Large multicentre studies are needed to confirm these findings and to elucidate the mechanisms by which hMPV potentiates the virulence and invasive capacity of diverse bacteria.


id: cord-307213-i8yijbiu
author: Ip, Jonathan Daniel
date: 2020-11-02
url: https://doi.org/10.1016/j.cmi.2020.10.030
doi: 10.1016/j.cmi.2020.10.030
title:
  Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain

abstract:
  OBJECTIVES: SARS-CoV-2 has evolved rapidly into several genetic clusters. However, data on mutations during the course of infection are scarce. This study aims to determine viral genome diversity in serial samples of COVID-19 patients. METHODS: Targeted deep sequencing of spike gene was performed on serial respiratory specimens from COVID-19 patients using nanopore and Illumina sequencing. Sanger sequencing was then performed to confirm the single nucleotide polymorphisms. RESULTS: A total of 28 serial respiratory specimens from 12 patients were successfully sequenced using nanopore and Illumina sequencing. A 75-year-old patient with severe disease had a mutation, G22017T, identified in the second specimen. The frequency of G22017T increased from ≤5% (nanopore: 3.8%; Illumina: 5%) from first respiratory tract specimen (sputum) to ≥60% (nanopore: 67.7%; Illumina: 60.4%) in the second specimen (saliva; collected 2 days after the 1(st) specimen). The difference in G22017T frequency was also confirmed by Sanger sequencing. G22017T corresponds to W152L amino acid mutation in the spike protein which was only found in <0.03% of the sequences deposited into a public database. Spike amino acid residue 152 is located within the N-terminal domain, which mediates the binding of a neutralizing antibody. CONCLUSIONS: A spike protein amino acid mutation W152L located within a neutralizing epitope has appeared naturally in a patient. Our study demonstrated that monitoring of serial specimens is important in identifying hotspots of mutations, especially those occurring at neutralizing epitopes which may affect the therapeutic efficacy of monoclonal antibodies.


id: cord-307273-pplky6g4
title: Homeless people hospitalized with COVID-19 in Brussels
author: Schrooyen, Loïc
date: 2020-08-07
txt: ./txt/cord-307273-pplky6g4.txt
cache: ./cache/cord-307273-pplky6g4.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1198743X2030478X
doi: 10.1016/j.cmi.2020.08.002
abstract: nan
summary:
  To the editor, Compared to the general population, homeless people have higher mortality, both related to communicable and non-communicable diseases, partly explained by higher exposure to risk factors including alcoholism, illicit drug abuse and smoking(1,2). Between 3 rd March and 26 th May 2020, 14 homeless people were identified among 238 patients hospitalized for a COVID-19 pneumonia resulting in a homelessness prevalence of 5.88%. Incidences of COVID-19 among homeless and non-homeless patients were calculated using homeless census report and our hospital catchment population. For the reporting period, incidences were 650 and 194/100.000 hospitalized homeless and non-homeless patients for COVID-19, respectively. We found a high but similar proportion of comorbidities (arterial hypertension, diabetes and cardiovascular diseases) in both populations hospitalized with COVID-19. The high prevalence of comorbidities and the increased exposure to risk factors in the homeless population could increase their risk of more severe disease and mortality following SARS-CoV-2 infection.


id: cord-314808-ssiggi2z
title: Psychosocial consequences of infectious diseases
author: Pappas, G.
date: 2014-12-12
txt: ./txt/cord-314808-ssiggi2z.txt
cache: ./cache/cord-314808-ssiggi2z.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1198743X14604614
doi: 10.1111/j.1469-0691.2009.02947.x
summary:
  On the other hand, numerous new major threats have emerged during the last three decades; the pandemic of AIDS, the SARS outbreak, the ominous scenarios of an avian influenza pandemic, and the threat of biological weapons are just some examples explaining the concern among health authorities, the media, and the public. The psychological response of both patients and the public to the threat of infection has been evaluated with respect to numerous circumstances in recent years, not only acute outbreaks such as SARS, but also gradually evolving pandemics such as AIDS, threats with marginal risk for humans such as bovine spongiform encephalopathy (BSE; mad cow disease), and even threats that are only theoretical such as avian influenza. Mass media is another major factor that shapes the physical and psychological response of the public to an infectious disease threat, as depicted in numerous attack scenarios in the literature [32] [33] [34] .

abstract:
  Historically, there has been an exaggerated fear related to infection compared to other conditions. Infection possesses unique characteristics that account for this disproportionate degree of fear: it is transmitted rapidly and invisibly; historically, it has accounted for major morbidity and mortality; old forms re-emerge and new forms emerge; and both the media and society are often in awe. Because, in an outbreak, the patient is both a victim and a vector, and because there exists the potential for infringement of personal rights in order to control an outbreak, infection may be viewed (and has been depicted in popular culture) as a foreign invasion. During recent outbreaks, fear, denial, stigmatization and loss have been recorded in the implicated individuals. Stigmatization and discrimination may further involve ethical correlations, and attempts to adress these issues through activism may also have unwarranted effects. Public health initiatives can address the public's fears by increasing health literacy, which can contribute to reducing stigmatization.


id: cord-317918-pl625ela
title: Secondary Infections in Patients Hospitalized with COVID-19: Incidence and Predictive Factors
author: Ripa, Marco
date: 2020-10-24
url: https://www.sciencedirect.com/science/article/pii/S1198743X20306522?v=s5
doi: 10.1016/j.cmi.2020.10.021
abstract:
  OBJECTIVES: Aim of our study was to describe the incidence and predictive factors of secondary infections in patients with COVID-19. METHODS: Cohort study on patients hospitalized with COVID-19 at IRCCS San Raffaele Hospital between February 25(th) and April 6th, 2020 (NCT04318366). We considered secondary bloodstream (BSIs) or possible lower respiratory tract infections (pLRTIs) occurred after 48 hours since hospital admission until death or discharge. We calculated multivariable Fine-Gray models, to assess factors associated with risk of secondary infections. RESULTS: Among 731 patients, a secondary infection was diagnosed in 68 patients (9.3%): 58/731 patients (7.9%) had at least one BSI and 22/731 patients (3.0%) at least one pLRTI. Overall 28-day cumulative incidence was 16.4% (95% CI 12.4% - 21.0%). The majority of BSIs was due to gram-positive pathogens (76/106 isolates, 71.7%), specifically coagulase-negative staphylococci (53/76, 69.7%), while among gram-negatives (23/106, 21.7%) Acinetobacter baumanii (7/23, 30.4%) and Escherichia coli (5/23, 21.7%) predominated. pLRTIs were mainly caused by gram-negative pathogens (14/26, 53.8%). Eleven patients were diagnosed with putative invasive aspergillosis. At multivariable analysis, factors associated with secondary infections were low baseline lymphocyte count (<0.7 vs >0.7 per 10(9)/L: subdistribution hazard ratios (sdHRs) 1.93 [95% CI 1.11-3.35]), baseline PaO(2)/FiO(2) (per 100-points lower: sdHRs 1.56 [95% CI 1.21-2.04]), and intensive-care unit (ICU) admission in the first 48 hours (sdHR 2.51 [95% CI 1.04-6.05]). CONCLUSIONS: Patients hospitalized with COVID-19 had a high incidence of secondary infections. At multivariable analysis, early need for ICU, respiratory failure, and severe lymphopenia, were identified as risk factors for secondary infections.


id: cord-318021-4qrf5m8s
author: Wolfensberger, A.
date: 2019-03-25
txt: ./txt/cord-318021-4qrf5m8s.txt
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extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1198743X19301211
doi: 10.1016/j.cmi.2019.03.019
summary:
  title: Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention() OBJECTIVES: Conducting manual surveillance of non-ventilator-associated hospital-acquired pneumonia (nvHAP) using ECDC (European Centre for Disease Prevention and Control) surveillance criteria is very resource intensive. Sensitivity, negative predictive value, and accuracy of semi-automated surveillance versus full manual surveillance were lowest in the validation sample consisting of patients with HAP according to the International Classification of Diseases (ICD-10) discharge diagnostic codes, with 97.5% (CI: 93.7–99.3%), 99.2% (CI: 97.9–99.8%), and 99.4% (CI: 98.4–99.8%), respectively. Three authors reported nvHAP incidence rates between 0.12 and 2.28 per 1000 patient days by applying the 2013 CDC surveillance definition to patients with International Classification of Diseases (ICD-9-CM) codes for pneumonia not present on admission [8e10] .

title:
  Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention()

abstract:
  OBJECTIVES: Conducting manual surveillance of non-ventilator-associated hospital-acquired pneumonia (nvHAP) using ECDC (European Centre for Disease Prevention and Control) surveillance criteria is very resource intensive. We developed and validated a semi-automated surveillance system for nvHAP, and describe nvHAP incidence and aetiology at our hospital. METHODS: We applied an automated classification algorithm mirroring ECDC definition criteria to distinguish patients ‘not at risk’ from patients ‘at risk’ for suffering from nvHAP. ‘At risk’-patients were manually screened for nvHAP. For validation, we applied the reference standard of full manual evaluation to three validation samples comprising 2091 patients. RESULTS: Among the 39 519 University Hospital Zurich inpatient discharges in 2017, the algorithm identified 2454 ‘at-risk’ patients, reducing the number of medical records to be manually screened by 93.8%. From this subset, nvHAP was identified in 251 patients (0.64%, 95%CI: 0.57–0.73). Sensitivity, negative predictive value, and accuracy of semi-automated surveillance versus full manual surveillance were lowest in the validation sample consisting of patients with HAP according to the International Classification of Diseases (ICD-10) discharge diagnostic codes, with 97.5% (CI: 93.7–99.3%), 99.2% (CI: 97.9–99.8%), and 99.4% (CI: 98.4–99.8%), respectively. The overall incidence rate of nvHAP was 0.83/1000 patient days (95%CI: 0.73–0.94), with highest rates in haematology/oncology, cardiac and thoracic surgery, and internal medicine including subspecialties. CONCLUSIONS: The semi-automated surveillance demonstrated a very high sensitivity, negative predictive value, and accuracy. This approach significantly reduces manual surveillance workload, thus making continuous nvHAP surveillance feasible as a pivotal element for successful prevention efforts.


id: cord-322585-5gio6ruj
title: Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise
author: Lanari, Marcello
date: 2020-06-25
url: https://doi.org/10.1016/j.cmi.2020.06.017
doi: 10.1016/j.cmi.2020.06.017
abstract:
  In this commentary, we focus our attention on what is known about SARS-CoV-2 infection in the pediatric population. We report literature and National data. The possible and different explanations for understanding why the infection seems to be more benign and less frequent in children are discussed. The possible role of children in the COVID-19 viral disease pandemic is also commented. Finally, our work suggests to search for future evidence and containment strategies to manage virus spread.


id: cord-324148-bllyruh8
author: Loubet, Paul
date: 2020-04-10
url: https://www.sciencedirect.com/science/article/pii/S1198743X20301907?v=s5
doi: 10.1016/j.cmi.2020.04.005
title:
  Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study

abstract:
  OBJECTIVES: To describe the prevalence, clinical features and complications of human metapneumovirus (hMPV) infections in a population of adults hospitalized with influenza-like illness (ILI). METHODS: This was a retrospective, observational, multicenter cohort study using prospectively collected data from adult patients hospitalized during influenza virus circulation, for at least 24h, for community-acquired ILI (with symptom onset <7 days). Data were collected from five French teaching hospitals over six consecutive winters (2012-2018). Respiratory viruses were identified by multiplex RT-PCR on nasopharyngeal specimens. hMPV+ patients were compared to hMPV– patients, influenza+ and respiratory syncytial virus (RSV)+ patients using multivariate logistic regressions. Primary outcome was the prevalence of hMPV in patients hospitalized for ILI. RESULTS: Among the 3148 patients included (1449 (46%) women, 1988 (63%) aged 65 and over; 2508 (80%) with chronic disease), at least one respiratory virus was detected in 1604 (51%, 95%CI [49-53]), including 100 cases of hMPV (100/3148, 3% 95%CI [3, 4]), of which 10 (10%) were viral co-infection. In the hMPV+ patients, mean length of stay was 7 days, 62% (56/90) developed a complication, 21% (14/68) were admitted to intensive care unit and 4% (4/90) died during hospitalization. In comparison with influenza+ patients, hMPV+ patients were more frequently > 65 years old (aOR=3.3, 95%CI[1.9-6.3]) and presented more acute heart failure during hospitalization (aOR=1.8, 95%CI[1.0-2.9]). Compared to RSV+ patients, hMPV+ patients had less cancer (aOR=0.4, 95%CI[0.2-0.9]) and were less likely to smoke (aOR=0.5, 95%CI[0.2-0.9]) but had similar outcomes especially high rate of respiratory and cardiovascular complications. CONCLUSIONS: Adult hMPV infections mainly affect the elderly and patients with chronic conditions and are responsible for frequent cardiac and pulmonary complications similar to those of RSV infections. At-risk populations would benefit from the development of antivirals and vaccines targeting hMPV.


id: cord-325186-nq6ay4eo
title: Recommendations for antibacterial therapy in adults with COVID-19 – An evidence based guideline
author: Sieswerda, Elske
date: 2020-10-01
txt: ./txt/cord-325186-nq6ay4eo.txt
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extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1198743X20305942?v=s5
doi: 10.1016/j.cmi.2020.09.041
summary:
  SCOPE: The Dutch Working Party on Antibiotic Policy constituted a multidisciplinary expert committee to provide evidence-based recommendation for the use of antibacterial therapy in hospitalized adults with a respiratory infection and suspected or proven 2019 Coronavirus disease (COVID-19). QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS: We assessed evidence on the risk of bacterial infections in hospitalized COVID-19 patients, the associated bacterial pathogens, how to diagnose bacterial infections and how to treat bacterial infections. For patients with secondary bacterial respiratory infection we recommend to follow other guideline recommendations on antibacterial treatment for patients with hospital-acquired and ventilator-associated pneumonia. An antibiotic treatment duration of five days in patients with COVID-19 and suspected bacterial respiratory infection is recommended upon improvement of signs, symptoms and inflammatory markers. As COVID-19 patients frequently 72 need prolonged hospitalization and respiratory support, unnecessary antibiotics upon 73 hospitalization may increase the individual risk of subsequent hospital-acquired pneumonia 74 (HAP) and other adverse events [12, 13] .

abstract:
  SCOPE: The Dutch Working Party on Antibiotic Policy constituted a multidisciplinary expert committee to provide evidence-based recommendation for the use of antibacterial therapy in hospitalized adults with a respiratory infection and suspected or proven 2019 Coronavirus disease (COVID-19). METHODS: We performed a literature search to answer four key questions. The committee graded the evidence and developed recommendations by using Grading of Recommendations Assessment, Development, and Evaluation methodology. QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS: We assessed evidence on the risk of bacterial infections in hospitalized COVID-19 patients, the associated bacterial pathogens, how to diagnose bacterial infections and how to treat bacterial infections. Bacterial co-infection upon admission was reported in 3.5% of COVID-19 patients, while bacterial secondary infections during hospitalization occurred up to 15%. No or very low quality evidence was found to answer the other key clinical questions. Although the evidence base on bacterial infections in COVID-19 is currently limited, available evidence supports restrictive antibiotic use from an antibiotic stewardship perspective, especially upon admission. To support restrictive antibiotic use, maximum efforts should be undertaken to obtain sputum and blood culture samples as well as pneumococcal urinary antigen testing. We suggest to stop antibiotics in patients who started antibiotic treatment upon admission when representative cultures as well as urinary antigen tests show no signs of involvement of bacterial pathogens after 48 hours. For patients with secondary bacterial respiratory infection we recommend to follow other guideline recommendations on antibacterial treatment for patients with hospital-acquired and ventilator-associated pneumonia. An antibiotic treatment duration of five days in patients with COVID-19 and suspected bacterial respiratory infection is recommended upon improvement of signs, symptoms and inflammatory markers. Larger, prospective studies about the epidemiology of bacterial infections in COVID-19 are urgently needed to confirm our conclusions and ultimately prevent unnecessary antibiotic use during the COVID-19 pandemic.


id: cord-325529-pid58g2r
title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection
author: Ben-Ami, Roni
date: 2020-06-23
url: https://www.sciencedirect.com/science/article/pii/S1198743X20303499?v=s5
doi: 10.1016/j.cmi.2020.06.009
abstract:
  OBJECTIVES: Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck, while the need to increase testing throughput only rises. We aim to overcome these challenges by pooling samples together, performing RNA extraction and RT-PCR in pools. METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of 8 samples in large-scale clinical tests. RESULTS: We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of 8 samples, showed that test results were not significantly affected. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. CONCLUSIONS: Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations.


id: cord-326341-egtnqlov
author: Liotti, Flora Marzia
date: 2020-09-23
txt: ./txt/cord-326341-egtnqlov.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1198743X20305838
doi: 10.1016/j.cmi.2020.09.030
abstract: nan
summary:
  title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples Conversely, rapid antigen detection assays-intrinsically less laborious and requiring few minutes 29 to results-have the potential to satisfy the pressing demand for an early SARS-CoV-2 infection 30 Suwon, South Korea) assay, a fluorescent immunoassay detecting SARS-CoV-2 nucleoprotein 33 antigen, on nasopharynx swab samples. The LOD was 5 × 10 2 41 TCID 50 /mL (2 × 10 6 RNA copies/mL) at 95% detection probability ( Supplementary Fig. S1 Our study shows that the STANDARD F COVID-19 Ag FIA assay had a good specificity for 65 SARS-CoV-2 detection in nasopharynx swab samples but had a good sensitivity only for samples 66 Evaluation of a rapid diagnostic assay for detection of SARS-CoV-102 2 antigen in nasopharyngeal swabs Evaluation of rapid 104 antigen test for detection of SARS-CoV-2 virus

title:
  Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples


id: cord-326703-akn92p1r
author: Bartoletti, Michele
date: 2020-08-08
url: https://www.ncbi.nlm.nih.gov/pubmed/32781244/
doi: 10.1016/j.cmi.2020.08.003
title:
  Development and validation of a prediction model for severe respiratory failure in hospitalized patients with SARS-Cov-2 infection: a multicenter cohort study (PREDI-CO study)

abstract:
  OBJECTIVES: We aimed to develop and validate a risk score to predict severe respiratory failure (SRF) among patients hospitalized with coronavirus disease-2019 (COVID-19). METHODS: We performed a multicentre cohort study among hospitalized (>24 hours) patients diagnosed with COVID-19 from February 22 to April 3 2020, at 11 Italian hospitals. Patients were divided into derivation and validation cohorts according to random sorting of hospitals. SRF was assessed from admission to hospital discharge and was defined as: SpO2<93% with 100% FiO2, respiratory rate (RR)>30bpm, or respiratory distress. Multivariable logistic regression models were built to identify predictors of SRF, β-coefficients were used to develop a risk score. Trial Registration NCT04316949. RESULTS: We analyzed 1113 patients (644 derivation, 469 validation cohort). Mean (±standard deviation)age was 65.7(±15) years, 704 (63.3%) were male. SRF occurred in 189/644 (29%) and 187/469 (40%) patients in derivation and validation cohort, respectively. At multivariate analysis, risk factors for SRF in the derivation cohort assessed at hospitalization were age ≥70 years [OR 2.74 (95%CI 1.66-4.50)], obesity [OR 4.62 (95%CI 2.78-7.70)], body temperature ≥38°C [OR 1.73 (95%CI 1.30-2.29)], RR ≥22bpm [OR 3.75 (95%CI 2.01-7.01)], lymphocytes ≤900/mm(3) [OR 2.69 (95%CI 1.60-4.51)], creatinine ≥1 mg/dl [OR 2.38 (95%CI 1.59-3.56)], C-reactive protein ≥10mg/dl [OR 5.91 (95%CI 4.88-7.17)], and lactate dehydrogenase ≥350IU/L[OR 2.39 (95%CI 1.11-5.11)]. Assigning points to each variable an individual risk score (PREDI-CO score) was obtained. Area under receiver-operator curve (AUROC) was 0.89 (0.86-0.92). At score of >3, sensitivity, specificity, positive and negative predictive values were 71.6%(65-79%), 89.1% (86-92%), 74%(67-80%), and 89%(85-91%), respectively;. PREDI-CO score showed similar prognostic ability in the validation cohort: AUROC 0.85 (0.81-0.88). At score of >3, sensitivity, specificity, positive and negative predictive values were 80% (73-85%), 76 (70-81%), 69%(60-74%) and 85% (80-89%), respectively. CONCLUSION: PREDI-CO score can be useful to allocate resources and prioritize treatments during COVID-19 pandemic.


id: cord-327253-gge6wzly
title: Stigma at the time of the COVID-19 pandemic
author: Villa, Simone
date: 2020-08-07
txt: ./txt/cord-327253-gge6wzly.txt
cache: ./cache/cord-327253-gge6wzly.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32777361/
doi: 10.1016/j.cmi.2020.08.001
abstract: nan
summary:
  1 Beginning in late January 2020, when the COVID-19 epidemic was still largely limited to China, verbal and physical attacks against Chinese or people of Asian descent have been documented in many countries. 10 In contrary, uninfected COVID-19 people may be facing discrimination when applying for jobs in some countries that may implement COVID-19 passport strategies, despite recommendations of the World Health Organization against such a practice. This reactive behaviour facilitates spreading of infectious pathogens especially among those with mild symptoms who avoid seeking medical attention and act J o u r n a l P r e -p r o o f as usual not to raise suspicion on their condition. The world cannot bear a parallel pandemic of stigma, which only serves to boost the spread of infectious diseases and worsen people''s health conditions and social behaviours. Noteworthy, individuals with COVID-19 may develop poor health-seeking behaviours (e.g. avoiding testing) because, by anticipating and fearing stigma, they may perceive the risk of losing their job and being marginalised in the society.


id: cord-328499-d6cvaxm9
title: Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2
author: Matzkies, Lucie-Marie
date: 2020-07-08
url: https://doi.org/10.1016/j.cmi.2020.06.036
doi: 10.1016/j.cmi.2020.06.036
abstract:
  OBJECTIVES: New molecular tests for SARS-CoV-2 are rapidly launched in response to the COVID-19 pandemic. The aim of this study was to evaluate the analytical and the clinical performance of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. METHODS: For testing the analytical performance, reference material was used. Clinical samples (n=101) obtained from patients with symptoms compatible to COVID-19 were studied. Oro- and nasopharyngeal swabs were collected by using either ESwab™ or UTM™ collection systems. RESULTS: When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test while results obtained with the cobas® test were found to be concordant with the results expected. Six out of the 101 clinical samples (5.9%) showed an inhibition with the VIASURE test. When analyzing the remaining 95 clinical samples, 27 were found to be negative with both assays. Of 68 samples positive with the cobas® test, the VIASURE test missed 21 (30.9 %) samples. All of those 21 samples had shown Ct values ≥ 31 with the cobas® 6800 system. None of the samples tested positive with the VIASURE test and negative with the cobas® test. CONCLUSIONS: The VIASURE test was impaired by a lack of sensitivity and a relatively high number of invalid results. When using the VIASURE test for routine testing, a significant number of COVID-19 positive samples would have been missed.


id: cord-329350-qrxl5o1e
author: Pan, Angelo
date: 2020-06-09
url: https://www.sciencedirect.com/science/article/pii/S1198743X20303360?v=s5
doi: 10.1016/j.cmi.2020.05.038
abstract: nan
title:
  Suggestions from Cremona, Italy - two months into the pandemic at the frontline of COVID-19 in Europe


id: cord-331002-7uojryqz
title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients
author: Valent, Francesca
date: 2020-09-06
url: https://api.elsevier.com/content/article/pii/S1198743X20305255
doi: 10.1016/j.cmi.2020.08.041
abstract:
  OBJECTIVES: Duration of SARS-CoV-2 in upper respiratory tract is extremely variable, but its relation to disease severity is unknown. We investigated such relation in the 530,000-inhabitant North-Eastern Italian province of Udine. METHODS: We analysed real‐time reverse‐transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 on upper respiratory specimens conducted at the Virology Laboratory of the University Hospital of Udine, Italy, serving the whole province, from March 1 to April 30, 2020, on positive subjects of four groups characterized by different disease severity (critically ill patients admitted to Intensive Care Units, patients admitted to Infectious Disease Units, symptomatic patients visited at the Emergency Department and not hospitalized, and asymptomatic subjects tested during contact tracing or screening activities). Duration of viral positivity was assessed from the first positive test to the day of the first of two consecutive negative tests. Univariate and multivariate analyses were conducted to investigate differences in the four groups. RESULTS: From March 1 to April 30, 39,483 RT-PCR tests for SARS-CoV-2 were conducted on 23,778 persons. 974 subjects had a positive test result. Among those with multiple tests (N=878), mean time to negativity was 23.7 days (standard error 0.3639) (median 23, interquartile range: 16-30 days). Mean time to negativity was longer in the ICU group than in the others, whereas no difference was observed between asymptomatic patients and those with mild disease. CONCLUSIONS: Disease control measures should not be adjusted to account for differences in viral shedding according to symptomatic status.


id: cord-333334-90q1xkld
author: Shengchen, D.
date: 2019-06-20
url: https://doi.org/10.1016/j.cmi.2019.06.012
doi: 10.1016/j.cmi.2019.06.012
title:
  Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial

abstract:
  OBJECTIVES: The primary objective was to evaluate whether a molecular point-of-care test (POCT) for viral and atypical pathogens added to routine real-time PCR could reduce duration of intravenous antibiotics in hospitalized patients with lower respiratory tract infection (LRTI) compared with routine real-time PCR. METHODS: In this single-centre, open-label, randomized controlled study, we enrolled hospitalized adults diagnosed with LRTI. Patients were randomized to an intervention group (POCT FilmArray Panel for 20 viruses, atypical pathogens and bacteria plus routine real-time PCR) or a control group (routine real-time PCR for ten pathogens). The primary outcome was duration of intravenous antibiotics during hospitalization. The secondary outcomes included length of stay, cost of hospitalization and de-escalation within 72 hours and between 72 hours and 7 days. Intention-to-treat analysis was used. RESULTS: Between October 2017 and July 2018, we enrolled 800 eligible patients (398 in the intervention group and 402 in the control group). Duration of intravenous antibiotics in the intervention group was shorter than in the control (7.0 days (interquartile range (IQR) 5.0–9.0) versus 8.0 days (IQR 6.0–11.0); p <0.001). Length of hospital stay in the intervention group was significantly shorter (8.0 days (IQR 7.0–11.0) versus 9.0 days (IQR 7.0–12.0; p <0.001) and the cost of hospitalization in the intervention group was significantly lower ($1804.7 (IQR 1298.4–2633.8) versus $2042.5 (IQR 1427.4–2926.2); p 0.002) than control group. More patients in the intervention group achieved de-escalation within 72 hours (7.9%, 29/367 versus 3.2%, 12/377; p 0.005) and between 72 hours and 7 days (29.7%, 109/367 versus 22.0%, 83/377; p 0.024). CONCLUSIONS: Use of molecular POCT testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in hospitalized LRTI patients. CLINICAL TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT03391076.


id: cord-334835-j6u8t8j2
author: Berenguer, Juan
date: 2020-08-04
txt: ./txt/cord-334835-j6u8t8j2.txt
cache: ./cache/cord-334835-j6u8t8j2.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.cmi.2020.07.024
doi: 10.1016/j.cmi.2020.07.024
summary:
  title: Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain OBJECTIVES: We aimed to analyse the characteristics and predictors of death in hospitalized patients with COVID-19 in Spain. Seventeen factors were independently associated with an increased hazard of death, the strongest among them included advanced age, liver cirrhosis, low age-adjusted oxygen saturation, higher concentrations of C-reactive protein, and lower estimated glomerular filtration rate. In the 209 final adjusted analysis, we found 17 factors independently associated with an increased hazard of 210 death: male sex, older age, arterial hypertension, obesity, liver cirrhosis, chronic neurological 211 disorder, active cancer, dementia, dyspnoea, confusion, low age-adjusted SaO2 on room air, higher 212 white cell blood count (WBC), higher neutrophil-to-lymphocyte ratio, lower platelet count, 213 prolonged INR, lower eGFR, and higher concentrations of CRP (Figure 2) .

title:
  Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain

abstract:
  OBJECTIVES: We aimed to analyse the characteristics and predictors of death in hospitalized patients with COVID-19 in Spain. METHODS: Retrospective observational study of the first consecutive patients hospitalized with COVID-19 confirmed by real-time polymerase chain reaction (RT-PCR) assay in 127 Spanish centres until March 17, 2020. The follow-up censoring date was April 17, 2020. We collected demographic, clinical, laboratory, treatment, and complications data. The primary endpoint was all-cause mortality. Univariable and multivariable Cox regression analyses were performed to identify factors associated with death. RESULTS: Of the 4,035 patients, males accounted for 2,433/3,987 (61.0%), the median age was 70 years, and 2,539/3,439 (73.8%) had >1 comorbidity. The most common symptoms were a history of fever, cough, malaise, and dyspnoea. During hospitalization 1,255/3,979 (31.5%) patients developed acute respiratory distress syndrome, 736/3,988 (18.5%) were admitted to intensive care units, and 619/3,992 (15.5%) underwent mechanical ventilation. Viral or host-targeted medications included lopinavir/ritonavir 2,820/4,005 (70.4%), hydroxychloroquine 2,618/3,995 (65.5%), interferon-beta 1,153/3,950 (29.2%), corticosteroids 1,109/3,965 (28.0%), and tocilizumab 373/3,951 (9.4%). Overall 1,131/4,035 (28%) patients died. Mortality increased with age (85.6% occurring in older than 65 years). Seventeen factors were independently associated with an increased hazard of death, the strongest among them included advanced age, liver cirrhosis, low age-adjusted oxygen saturation, higher concentrations of C-reactive protein, and lower estimated glomerular filtration rate. CONCLUSIONS: Our findings provide comprehensive information about characteristics and complications of severe COVID-19 and may help to identify patients at a higher risk of death.


id: cord-343090-dsjq98ks
title: Review of trials currently testing treatment and prevention of COVID-19
author: Fragkou, Paraskevi C.
date: 2020-05-23
url: https://www.sciencedirect.com/science/article/pii/S1198743X20302962?v=s5
doi: 10.1016/j.cmi.2020.05.019
abstract:
  BACKGROUND: As COVID-19 cases continue to rise globally, evidence from large randomised controlled trials is still lacking. Currently, numerous trials testing potential treatment and preventative options are undertaken all over the world. OBJECTIVES: We summarised all registered clinical trials examining treatment and prevention options for COVID-19. Additionally, we evaluated the quality of the retrieved studies. DATA SOURCES: Clinicaltrials.gov, the Chinese Clinical Trial Registry and the European Union Clinical Trials Register were systematically searched. STUDY ELIGIBILITY CRITERIA: Registered clinical trials examining treatment and/or prevention options for COVID-19 were included. No language, country or study design restrictions were applied. We excluded withdrawn or cancelled studies and trials not reporting therapeutic or preventative strategies for COVID-19. PARTICIPANTS: and interventions: No restrictions in terms of participants’ age and medical background or type of intervention were enforced. METHODS: The registries were searched using the term “coronavirus” or “COVID-19” from their inception until 26(th) March 2020.Additional manual search of the registries was also performed. Eligible studies were summarised and tabulated. Interventional trials were methodologically analysed, excluding expanded access studies and trials testing Traditional Chinese Medicine. RESULTS: In total, 309 trials evaluating therapeutic management options, 23 studies assessing preventive strategies and 3 studies examining both were retrieved. Finally, 214 studies were methodologically reviewed. Interventional treatment studies were mostly randomised (n=150, 76%) and open-label (n=73, 37%) with a median number of planned inclusions of 90 (IQR 40-200). Major categories of interventions that are currently being investigated are discussed. CONCLUSION: Numerous clinical trials have been registered since the onset of the COVID-19 pandemic. Summarised data on these trials will assist physicians and researchers to promote patient care and guide future research efforts for COVID-19 pandemic containment.


id: cord-344027-qghktrm1
author: Fiolet, Thibault
date: 2020-10-17
txt: ./txt/cord-344027-qghktrm1.txt
cache: ./cache/cord-344027-qghktrm1.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1198743X20306133?v=s5
doi: 10.1016/j.cmi.2020.10.002
abstract: nan
summary:
  title: ''Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients'' – Author''s reply As with all studies at risk of critical bias included in our systematic review, it was excluded 50 from the main analysis. Treatment 154 with hydroxychloroquine, azithromycin, and combination in patients hospitalized with Clinical 158 Efficacy of Chloroquine derivatives in COVID-19 Infection: Comparative meta-analysis 159 between the Big data and the real world Hydroxychloroquine in Hospitalized Patients with COVID-19: Preliminary results from a 166 multi-centre, randomized, controlled trial COVID-19 177 prevention and treatment: A critical analysis of chloroquine and hydroxychloroquine 178 clinical pharmacology Interventions 188 for treatment of COVID-19: A living systematic review with meta-analyses and trial 189 sequential analyses (The LIVING Project) Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19: an 193 international collaborative meta-analysis of randomized trials Hydroxychloroquine as pre-exposure prophylaxis for COVID-19 in healthcare workers: 203 a randomized trial

title:
  ''Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients'' – Author’s reply


id: cord-344581-h7ikjgic
author: Ong, David S.Y.
date: 2020-06-02
txt: ./txt/cord-344581-h7ikjgic.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.cmi.2020.05.028
doi: 10.1016/j.cmi.2020.05.028
summary:
  OBJECTIVES: To assess the diagnostic performance of rapid lateral flow immunochromatographic assays (LFAs) compared to an enzyme-linked immunosorbent assay (ELISA) and nucleic acid amplification tests (NATs) in suspected coronavirus disease 2019 (COVID-19) patients. In the total cohort, Orient Gene Biotech COVID-19 IgG/IgM Rapid Test LFA had a sensitivity of 43/99 (43%; 95% CI 34-53) and specificity of 126/129 (98%; 95% CI 95-100). CONCLUSIONS: There is large variability in diagnostic test performance between rapid LFAs, but overall limited sensitivity and high specificity in acutely admitted patients. First, in a pilot phase 20 NAT-positive and 5 NAT-negative patients were retrospectively selected for which six LFAs were performed on heparin plasma samples obtained upon hospital presentation ( Figure S1 ), which corresponded to the dates of molecular testing. This study shows that the sensitivity of LFA was low in patients suspected for COVID-19 presenting to the hospital, but it improved in patients with at least seven days of symptoms and in those with CRP levels >100 mg/L upon presentation.

title:
  Comparison of diagnostic accuracies of rapid serological tests and ELISA to molecular diagnostics in patients with suspected COVID-19 presenting to the hospital

abstract:
  OBJECTIVES: To assess the diagnostic performance of rapid lateral flow immunochromatographic assays (LFAs) compared to an enzyme-linked immunosorbent assay (ELISA) and nucleic acid amplification tests (NATs) in suspected coronavirus disease 2019 (COVID-19) patients. METHODS: Patients presenting to a Dutch teaching hospital were eligible between March 17 and April 10, 2020, when they had respiratory symptoms that were suspected for COVID-19. The performances of six different LFAs were evaluated in plasma samples obtained on corresponding respiratory sample dates of NATs testing. Subsequently, the best performing LFA was evaluated in 228 patients and in 50 sera of a historical patient control group. RESULTS: In the pilot analysis sensitivity characteristics of LFA were heterogenous ranging from 2/20 (10%; 95% confidence interval (CI) 0-23) to 11/20 (55%; 95% CI 33-77). In the total cohort, Orient Gene Biotech COVID-19 IgG/IgM Rapid Test LFA had a sensitivity of 43/99 (43%; 95% CI 34-53) and specificity of 126/129 (98%; 95% CI 95-100). Sensitivity increased to 31/52 (60%; 95% CI 46-73) in patients with at least seven days of symptoms, and to 21/33 (64%; 95% CI 47-80) in patients with C-reactive protein (CRP) >100 mg/L. Sensitivity and specificity of Wantai SARS-CoV-2 Ab ELISA was 59/95 (62%; 95% CI 52-72) and 125/128 (98%; 95% CI 95-100) in all patients, respectively, but sensitivity increased to 38/48 (79%; 95% CI 68-91) in patients with at least seven days of symptoms. CONCLUSIONS: There is large variability in diagnostic test performance between rapid LFAs, but overall limited sensitivity and high specificity in acutely admitted patients. Sensitivity improved in patients with longer existing symptoms or high CRP. LFAs should only be considered as additional triage tools when these may lead to the improvement of hospital logistics.


id: cord-351028-p5cq2is5
title: Corticosteroid administration for viral pneumonia: COVID-19 and beyond
author: Yang, Jia-Wei
date: 2020-06-27
url: https://api.elsevier.com/content/article/pii/S1198743X20303645
doi: 10.1016/j.cmi.2020.06.020
abstract:
  BACKGROUND: Corticosteroids are commonly used as adjuvant therapy for acute respiratory distress syndrome (ARDS) by many clinicians due to their perceived anti-inflammatory effects. However, for patients with severe viral pneumonia, the corticosteroid treatment is highly controversial. OBJECTIVES: The purpose of this review is to systematically evaluate the effect and potential mechanism of corticosteroid administration in pandemic viral pneumonia. SOURCES: We comprehensively searched all manuscripts on corticosteroids therapy for influenza, SARS, MERS and SARS-CoV-2 viral pneumonia from the PubMed, EMBASE, Web of Science and Cochrane Library databases. CONTENT: We systematic summarized the effects of corticosteroids therapy for pandemic viral pneumonia and the potential mechanism of corticosteroid worked in COVID-19. IMPLICATIONS: Observational studies showed that corticosteroid treatment was associated with increased mortality and nosocomial infections for influenza and delay virus clearance for SARS-CoV and MERS-CoV. Limited data on corticosteroid therapy for COVID-19 were reported. Corticosteroids were used in about a fifth of patients (670/2995, 22.4%). Although clinical observational studies reported the improvement in symptoms and oxygenation for the severe COVID-19 patients received corticosteroids therapy, case fatality rate in the corticosteroid group was significantly higher than that in the non-corticosteroid group (69/443, 15.6% vs 56/1310, 4.3%). Compared with non-severe patients, severe patients were more likely to receive corticosteroid therapy (201/382, 52.6% vs 201/1310, 15.3%). Although there is no evidence of corticosteroid therapy reduce the mortality of COVID-19 patients, some improvements in clinical symptoms and oxygenation were reported in some clinical observational studies. Excessive inflammatory response and lymphopenia might be critical factors associated with disease severity and mortality of COVID-19. Sufficiently powered randomized controlled trials with rigorous inclusion/exclusion criteria and standardized dose and duration of corticosteroids are needed to verify the effectiveness and safety of corticosteroid therapy.


