# pos

id: cord-305583-p2jp5fiq
pos: NNP
token:
  http://www.nhsggc.org.uk/about-us/professional-supportsites/scottish-microbiology-reference-laboratories/

lemma:
  http://www.nhsggc.org.uk/about-us/professional-supportsites/scottish-microbiology-reference-laboratories/


# ent

id: cord-008695-y7il3hyb
type: DISEASE
entity:
  ischaemic heart disease Chronic renal disease Nephrotic syndrome chronic renal failure renal transplantation Chronic liver disease Cirrhosis inflammatory bowel disease Diabetes


id: cord-019982-hyxrgamj
type: ORG
entity:
  Muhimbili Hospital Paediatric Services University Department of Child Health and Paediatric Department


id: cord-019968-o5bdb37q
type: CL
entity:
  smooth and rough particles Flewett 1977 were 64 5 nm and 53 8 nm respectively standard deviation 2 4 nm and 4 3 nm respectively Rotavirus like particles that failed to agglutinate on IEM were seen in two gastroenteritis patients stools and in one control patient s stool Solitary particles indicated non agglutination Small round particles which I shali call satellite particles


id: cord-264255-q5izs39f
type: DISEASE
entity:
  human rhinoviruses paramyxoviruses coronaviruses and bocavirus during acute respiratory tract infection


id: cord-270258-9vgpphiu
type: PROTEIN
entity:
  lymphocyte count AST aspartate transaminase ALT alanine transaminase BUN blood urea nitrogen CRP C reactive protein LD lactate dehydrogenase Ct threshold cycle rRT


id: cord-254635-gtgahlqm
type: DISEASE
entity:
  influenza and respiratory syncytial virus in the United States Pandemic flu clinical management of patients with an influenza like illness


id: cord-008686-9ybxuy00
type: DISEASE
entity:
  influenza A B respiratory syncytial virus RSV parainfluenza PIV types 1 4 human metapneumo hMPV entero rhino corona 229E OC43 NL63 HKU1


id: cord-288814-1zayb21f
type: WORK_OF_ART
entity:
  WHO Report of the WHO China Joint Mission on Coronavirus Disease Characteristics of and Important Lessons From the Coronavirus Disease 2019 COVID 19 Outbreak


id: cord-288814-1zayb21f
type: DISEASE
entity:
  chronic obstructive pulmonary diseases COPD malignancy cerebrovascular diseases CVD chronic kidney diseases CKD


id: cord-280188-gir0y1m1
type: DNA
entity:
  China date 2016 06 13 journal J Infect DOI 10 1016 j jinf 2016 05 014 sha 8041d43c81822cc671336b37a3a7d93e1a24e663 doc_id 280188 cord_uid gir0y1m1


id: cord-280350-ay4cnzn5
type: ORG
entity:
  Chemical Genetics Unit Department of Microbiology Research Center of Infection and Immunology Li Kashing Faculty of Medicine the University of Hong Kong


id: cord-280350-ay4cnzn5
type: CHEMICAL
entity:
  mycophenolic acid flufenamic acid tolfenamic acid meclofenamate sodium mefenamic acid ribavirin mercaptopurine pyrimethamine emetine


id: cord-280350-ay4cnzn5
type: CHEMICAL
entity:
  glycyrrhizin baicalin reserpine aescin valinomycin niclosamide aurintricarboxylic acid mizoribine indomethacin chloroquine


id: cord-281130-9tawihti
type: GGP
entity:
  LDH r 0 62 p 0 001 CRP r 0 59 p 0 001 and D dimer r 0 43 p 0 001 Furthermore a multivariate logistic regression analysis using all considered variables confirmed the independent prognostic role of PTX3


id: cord-298639-v9yg80jw
type: DNA
entity:
  primer 5 CCCTGTGGGTTTTACACTTAA 3 reverse primer 5 ACGATTGTGCATCAGCTGA 3 probe 5ʹ VIC CCGTCTGCGGTATGTGGAAAGGTTATGG BHQ1 3ʹ


id: cord-292201-e7k7gn9q
type: PERSON
entity:
  Vega Wanyenze Rhoda K Dula Janeth Watanabe Takashi Delgado Ratto Christopher Driessche Koen Vanden Van


id: cord-295074-fsbp4fky
type: PROTEIN
entity:
  cord 295074 fsbp4fky authors Broor Shobha Dawood Fatimah S Pandey Bharti G Saha Siddhartha Gupta Vivek Krishnan Anand Rai Sanjay Singh Pratibha Erdman Dean Lal Renu B title


id: cord-295074-fsbp4fky
type: DISEASE
entity:
  influenza and parainfluenza viruses respiratory syncytial virus RSV human metapneumovirus coronaviruses and adenovirus Average annual hospitalization incidence was calculated using census data and adjusted for hospitalizations


id: cord-291561-sxvgue36
type: GGP
entity:
  polymyxin b hemoperfusion on 28 Day mortality in patients with septic shock and elevated endotoxin level the EUPHRATES


id: cord-291561-sxvgue36
type: ORG
entity:
  the National Major Science and Technology Project for Control and Prevention of Major Infectious Diseases


id: cord-290385-0smnl70i
type: PROTEIN
entity:
  lactate dehydrogenase aspartate aminotransferase g glutamyl transferase fibrinogen ferritin C reactive protein


id: cord-290385-0smnl70i
type: DISEASE
entity:
  coronaviruses severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus influenza viruses and Ebola virus 2e11


id: cord-290066-umthoftd
type: WORK_OF_ART
entity:
  Different Types of Clinical Specimens Potential False Negative Nucleic Acid Testing Results for Severe Acute Respiratory Syndrome Coronavirus 2 from Thermal Inactivation of Samples with Low Viral Loads Clinical


id: cord-305462-2wz1f6k6
type: DISEASE
entity:
  coronavirus OC43 and 229E 1 10 TCID 50 picornaviruses 1 TCID 50 adenoviruses 10 50 TCID 50 and human metapneumovirus 10 50 TCID 50 Table 2


id: cord-305462-2wz1f6k6
type: DISEASE
entity:
  influenza and respiratory syncytial virus in the United States Winter viruses influenza and respiratory syncytial virus related morbidity


id: cord-289364-p31gt533
type: WORK_OF_ART
entity:
  Transmission Diagnosis and Treatment of Coronavirus Disease Diagnostic Testing for Severe Acute Respiratory Syndrome Related


id: cord-303904-8ubm0kig
type: DISEASE
entity:
  respiratory syncytial virus RSV influenza A FluA influenza B FluB human rhinovirus HRV human metapneumovirus HMPV parainfluenza 1 2 3 and 4 PIV1 4 human coronaviruses OC43 and 229E HCoV enteroviruses EV human parechoviruses HPeV human bocavirus HBoV


id: cord-307333-n6jc0jy3
type: DNA
entity:
  IFN lambda 1 forward primer 5 0 GGACGCCTTGGAAGAGTCACT 3 0 reverse primer 5 0 AGAAGCCTCAGGTCCCAATTC 3 0 probe 5 0 FAM AGTTGCAGCTCTCCTGTCTTCCCCG 3 TAMRA 27 IFN lambda 2e3 forward primer 5 0 CTGCCACATAGCCCAGTTCA 3 0 reverse primer 5 0 AGAAGCGACTCTTCTAAGGCATCTT 3 pro be 5 0 FAM TCTCCACAGGAGCTGCAGGCCTTTA 3 TAMRA 27 MxA forward primer 5 0 CTGCCTGGCAGAAAAACTTAC 3 reverse primer 5 0 CTCTGTTATTCTCTGGTGAGTCTCCTT 3 0 probe 5 0 FAM CATCACACATATCTGTAAATCTCTGCCCCTGTT 3 TAMRA ISG56 forward primer 5 0 TGAAGAAGCTCTAGC CAACATGTC 3 0 reverse primer 5 0 GAGCTTTATCCACA GAGCCTTTTC 3 0 probe 6 FAM 5 0 TATGTCTTTCGATATG CAGCCAAGTTTTACCG 3 0 TAMRA 28


id: cord-307333-n6jc0jy3
type: DNA
entity:
  primer 5 0 TCTGTCAAGGGCAGTAACCTG 3 reverse primer 5 0 GCCCACGACTTTGTTTTCTG 3 0 probe 5 0 FAM TCAAGTTGGAAGTGCGTCTTTTGGATGC 3 TAMRA


id: cord-307333-n6jc0jy3
type: CHEMICAL
entity:
  interferon lambda 1 IFN lambda1 IL 29 Interferon lambda 1 IFN lambda1 IL 29 induces ELR CXC chemokine mRNA in human peripheral blood mononuclear


id: cord-303763-2784hze3
type: DISEASE
entity:
  influenza A H1N1 virus after vaccination with seasonal influenza vaccination The impact of sex gender and pregnancy


id: cord-291960-1is0rv6c
type: CELL_LINE
entity:
  BCYE alpha agar BD becston Dickinson MGIT Mycobacteria Growth Indicator Tube Lowenstein Jensen agar slants


id: cord-291960-1is0rv6c
type: ORG
entity:
  the European Organization for Research and Treatment of Cancer Invasive Fungal Infections Cooperative Group


id: cord-315300-v3pxb997
type: ORG
entity:
  COVID 19 National Health Commission of the People s Republic of China Guidelines for the Diagnosis and Treatment of COVID


id: cord-317846-str9i01o
type: LAW
entity:
  COVID 19 pneumonia Interpretation of Guidelines for the Diagnosis and Treatment of Novel Coronavirus 2019


id: cord-318126-gg68o52z
type: GGP
entity:
  SARS CoV 2 Early Identification and Prevention of the Spread of Ebola United States Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus


id: cord-312602-855n5av1
type: DNA
entity:
  C gattii genotype AFLP4 VGI C bacillisporus genotype AFLP5 VGIII C deuterogattii genotype AFLP6 VGII C tetragattii genotype


id: cord-312602-855n5av1
type: WORK_OF_ART
entity:
  Importance of Resolving Fungal Nomenclature the Case of Multiple Pathogenic Species in the Cryptococcus Genus Global Molecular Epidemiology of Cryptococcus


id: cord-322451-cwpz4akv
type: CELL_LINE
entity:
  Threat Scope Note U United States National Intelligence Center Severe acute respiratory syndrome SARS


id: cord-305583-p2jp5fiq
type: DISEASE
entity:
  fever lethargy malaise somnolence gastrointestinal symptoms nausea abdominal pain vomiting diarrhoea


id: cord-347280-jpwf55l6
type: PROTEIN
entity:
  serine protease 2 MCP1 CCL2 Monocyte chemoattractant protein 1 MIP 1α CCL3 Macrophage inflammatory protein 1 alpha


id: cord-311766-m9yv4qkm
type: ORG
entity:
  Biotime Biotechnology Co Autobio Diagnostics Co ISIA BIO Technology Co and Biolidics For the Biotime Autobio


# bib

id: cord-007562-4hcs0z65
author: Bijlenga, G.
date: 2005-07-19
txt: ./txt/cord-007562-4hcs0z65.txt
cache: ./cache/cord-007562-4hcs0z65.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119113/
doi: 10.1016/j.jinf.2005.04.010
abstract: nan
summary:
  title: Proposal for vaccination against SARS coronavirus using avian infectious bronchitis virus strain H from The Netherlands HBV DNA testing by NAT of all the collected units of blood should be adopted by all the blood banks, in order to possibly achieve zero risk of transfusion transmitted HBV infection and also to reduce the rejection rate of the precious units of collected blood by testing for anti HBc. The outbreak of severe acute respiratory syndrome (SARS) in 2003 has resulted in a number of infections and deaths among healthcare workers (HCWs) and those in contact with SARS-infected persons. Development and use of the H strain of avian infectious bronchitis virus from The Netherlands as a vaccine: a review Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus The carboxyl-terminal 120-residue polypeptide of infectious bronchitis virus nucleocapsid induces cytotoxic T lymphocytes and protect chickens from acute infection

title:
  Proposal for vaccination against SARS coronavirus using avian infectious bronchitis virus strain H from The Netherlands


id: cord-007926-um2khqhn
title: The continuous evolution and dissemination of 2019 novel human coronavirus
author: Zhang, Jiahao
date: 2020-02-22
txt: ./txt/cord-007926-um2khqhn.txt
cache: ./cache/cord-007926-um2khqhn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7127192/
doi: 10.1016/j.jinf.2020.02.001
abstract: nan
summary:
  With rapid dissemination of the 2019-nCoV, the viruses had been transmitted rapidly in more than 25 countries, and a steep increase in human infection with the 2019-nCoV occurred in China ( Fig. 1 ) . Most of the patients infected with novel 2019-nCoV had a history to the seafood and live animal markets, and the vendor used to sale wild animal species, including marmot, snake, leopard cat, bamboo rat, badger, and hedgehog in Huanan seafood wholesale market (Supplementary Figure S4 ), all of which were susceptible to the novel CoV in nature, indicating that it remains likely there was intermediate hosts in the transmission cascade from bats to humans ( Fig. 2 ) . Recently, the continuous interspecies transmission events of CoV occurred, including the emergence of MERS-CoV from camels to humans and swine acute diarrhea syndrome CoV from bat to swine, posing serious threats to public health.


id: cord-008671-k0vda7fy
title: Clinical features of rotavirus gastroenteritis
author: McCormack, J.G.
date: 2005-04-14
txt: ./txt/cord-008671-k0vda7fy.txt
cache: ./cache/cord-008671-k0vda7fy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133613/
doi: 10.1016/s0163-4453(82)93777-x
summary:
  A history of contact with an adult with diarrheoa, vomiting occuring before diarrhoea, accompanying upper respiratory tract infection (URTI), otitis media and pyrexia and the need for administration of intravenous fluids were all significantly more prominent features of the rotavirus than the non-specific cases of gastroenteritis, and are suggested as pointers to such a diagnosis. Although an outbreak ofrotavirus gastroenteritis has been described involving adults without the known infection of children, 8 the finding of rotaviruses in adult stools has usually been acompanied by no intestinal symptoms, zl The finding in this study of a significantly higher incidence of a history of contact with an adult with gastroenteritis in the rotavirus than in the non-specific cases would suggest that adults may represent a reservoir for potential rotavirus infection in infants. The failure to find rotaviruses in the stools of any control patients with similar infections, but without diarrhoea, would support the role of the rotavirus as being responsible for the intestinal features of such illnesses.

abstract:
  Five hundred and eighteen children under the age of five years admitted to hospital with a diagnosis of gastroenteritis over a twelve-month period were studied prospectively. Rotaviruses were demonstrated by stool electron microscopy (EM) in 132 of these cases (25·4 per cent), but in none of io8 age- and sex-matched controls. Non-specific cases, where no potentially pathogenic organism could be demonstrated in stools submitted for EM, viral and bacterial culture accounted for 46 per cent of cases. If EM of the stools had not been performed the proportion of non-specific cases would have risen to 85 per cent, thus demonstrating the importance of this technique in diagnosis. Rotaviruses were most commonly found in winter and between the ages of six and eighteen months. A history of contact with an adult with diarrheoa, vomiting occuring before diarrhoea, accompanying upper respiratory tract infection (URTI), otitis media and pyrexia and the need for administration of intravenous fluids were all significantly more prominent features of the rotavirus than the non-specific cases of gastroenteritis, and are suggested as pointers to such a diagnosis. Pneumonia is described in three patients as an accompanying illness with rotavirus gastroenteritis.


id: cord-008672-luoxomif
title: Chronic diarrhoea among HIV-infected adult patients in Nairobi, Kenya
author: Mwachari, C.
date: 2004-10-29
txt: ./txt/cord-008672-luoxomif.txt
cache: ./cache/cord-008672-luoxomif.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133614/
doi: 10.1016/s0163-4453(98)90561-8
summary:
  We undertook a prospective cross-sectional study of adult patients admitted to a government hospital in Nairobi, Kenya, to determine possible bacterial, mycobacterial, parasitic and viral causes of diarrhoca; to consider which may be treatable; and to relate microbiological findings to clinical outcome. METHODS: Stool specimens from 75 consecutive HIV-seropositive patients with chronic diarrhoca admitted to a Nairobi hospital were subjected to microbiological investigation and results were compared with clinical findings and outcome. CONCLUSIONS: HIV-infected patients with chronic diarrhoea in Nairobi have a poor outcome overall, and even with extensive investigation a putative pathogen was identified in only just over half the patients. We undertook a 4-month study in Nairobi, Kenya, to determine possible bacterial, viral and parasitological causes of chronic diarrhoea and wasting using a broad range of investigations and related findings to patient outcome.

abstract:
  OBJECTIVES: Chronic diarrhoea and wasting are well recognized features of AIDS in Africa. However, because of resource constraints few ocmprehensive aetiological studies have conducted in sub-Saharan Africa which have included a broad range of microbiological investigations. We undertook a prospective cross-sectional study of adult patients admitted to a government hospital in Nairobi, Kenya, to determine possible bacterial, mycobacterial, parasitic and viral causes of diarrhoca; to consider which may be treatable; and to relate microbiological findings to clinical outcome. METHODS: Stool specimens from 75 consecutive HIV-seropositive patients with chronic diarrhoca admitted to a Nairobi hospital were subjected to microbiological investigation and results were compared with clinical findings and outcome. Stool samples were cultured for bacteria and mycobacteria and underwent light and electron microscopy; lawns of Escherichica coli were probed for pathogenic types and aliquots were tested for the presence of Clostridium difficile cytotoxin. Blood cultures for mycobacteria and other bacterial pathogens were performed as clinically indicated. RESULTS: Thirty-nine (52%) patients yielded putative pathogens, the most common being Cryptosporidium sp. (17%), Salmonella typhimurium (13%), and Mycobacterium tuberculosis (13%). Of 41 patients investigated for pathogenic Escherichia coli, enteroaggregative E. coli and diffusely adherent E. coli were each found in four patients. Thirty-one (41%) patients died. Detection of cryptosporidium cysts was the single most significant predictor of death (X(2) = 5.2, P<0.05). Many patients did not improve (21; 285) or self-discharged whilst still sick (5; 7%) but five (7%) were diagnosed ante mortem with tuberculosis and treated and a further 13 (17%) showed improvement by time of discharge. CONCLUSIONS: HIV-infected patients with chronic diarrhoea in Nairobi have a poor outcome overall, and even with extensive investigation a putative pathogen was identified in only just over half the patients. The most important step is to exclude tuberculosis: and the most useful investigation appears to be Ziehl-Neelsen staining. Other potentially treatable Gram-negative bacterial pathogens, S. typhimurium, Shigella sp. and adherent E. coli were, however, common but require culture facilities which are not widely accessible for definitive identification. Further studies focussing on simple ways to identify sub-groups of patients with treatable infections are warranted.


id: cord-008676-35dgybwy
title: Severe respiratory disease with rhinovirus detection: Role of bacteria in the most severe cases
author: Armero, Georgina
date: 2016-08-05
txt: ./txt/cord-008676-35dgybwy.txt
cache: ./cache/cord-008676-35dgybwy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133628/
doi: 10.1016/j.jinf.2016.07.010
abstract: nan
summary:
  We read with interest a recent paper in this Journal about how the nasopharyngeal bacterial burden may influence in the severity in infants with respiratory syncytial virus (RSV) bronchiolitis. 1 We performed a study which aim was to analyze the epidemiologic and clinical characteristics of patients with severe lower-respiratory-tract infection (LRTI) with Rhinovirus (RV) detection in comparison to the patients without RV detection in a pediatric intensive care unit (PICU), and the role of viral and/or bacterial codetections as risk factors of severity. 3, 5 No differences in severity (requirements of ventilatory support, length of ventilatory support and PICU stay) were found between patients infected with RV and patients with other viral detections. 1 We feel that bacterial carriage in children with virus infection influences either in predisposing to bacterial pneumonia more easily (but 2 of 9 patients in our study do not fulfilled this criteria) or to suffer a greater airway inflammation such as Yu et al.


id: cord-008678-zi3aunqz
author: Piñana, José Luis
date: 2020-01-10
txt: ./txt/cord-008678-zi3aunqz.txt
cache: ./cache/cord-008678-zi3aunqz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133636/
doi: 10.1016/j.jinf.2020.01.001
abstract: nan
summary:
  All specimens tested negative by direct examination for PJ, whereas 27 were positive by real-time PCR (BAL, n = 18; sputa, n = 7, and TA, n = 2); Following stringent clinical, microbiological and imaging criteria ( Table 1 ) , PJP was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. In addition to its retrospective nature, our study also has some limitations: (i) we cannot completely rule out that some patients categorized as being PJ carriers The probability of Pneumocystis jirovecii (PJ) pneumonia (PJP) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented PJ presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-PJP treatment; (v) absence of alternative diagnosis.

title:
  Clinical significance of Pneumocystis jirovecii DNA detection by real-time PCR in hematological patient respiratory specimens


id: cord-008686-9ybxuy00
title: Poor transmission of seasonal cold viruses in a British Antarctic Survey base
author: Everett, Tom
date: 2019-03-14
txt: ./txt/cord-008686-9ybxuy00.txt
cache: ./cache/cord-008686-9ybxuy00.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133657/
doi: 10.1016/j.jinf.2019.03.007
abstract: nan
summary:
  However, in the acute infection stage respiratory viruses are generally present in relatively high copy numbers, with median values of mostly 4-8 log 10 (i.e. 10,0 0 0-10 0,0 0 0,0 0 0 copies/ml) for adeno-, corona-, hMPV, influenza, PIV and RSV, as reported in one comprehensive paediatric study. 2 A 26-year-old male ( index case of the outbreak report 2 ) from Kerala''s Perambra town died undiagnosed with fever, en-cephalitis and respiratory distress in Government Medical College Kozhikode(GMCK), after being transferred from Taluk Hospital, Perambra(THP). 6 Along with the wound cleansing and post-exposure rabies immunoglobulin (RIG) and vaccination, any risk of SHBV requires that high dose acyclovir (preferably valaciclovir 1 g TDS PO; or acyclovir 800 mg 5 times daily PO, for adults) PEP for at least 14 days should be considered. After the first dengue-fever epidemic in China, which occurred in May 1978 in Foshan, Guangdong Province, there have been regional outbreaks of dengue every year and the number of cases has increased.


id: cord-008695-y7il3hyb
author: nan
date: 2007-01-25
txt: ./txt/cord-008695-y7il3hyb.txt
cache: ./cache/cord-008695-y7il3hyb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133687/
doi: 10.1016/s0163-4453(07)60001-2
abstract: nan
summary:
  Children may be considered at increased risk of complications if they have cough and fever (or influenza-like illness) and temperature >38.5ºC, plus either chronic co-morbid disease or one of following features: breathing difficulties severe earache vomiting >24 hours drowsiness These patients should be offered an antibiotic as well as oseltamivir (in those >1 year of age) and advice on antipyretics and fluids. Children may be considered at increased risk of complications if they have: Cough and fever (or influenza-like illness) and temperature >38.5ºC and either (i) chronic co-morbid disease (see Appendix 2) or (ii) one of the following features • Breathing difficulties • Severe earache • Vomiting > 24 hours • Drowsiness These patients should be offered an antibiotic as well as oseltamivir (in those over one year of age) and advice on antipyretics and fluids.

title:
  Pandemic Flu: Clinical management of patients with an influenza-like illness during an influenza pandemic


id: cord-010536-9ea7vvsz
author: Chu, Yanan
date: 2020-04-28
txt: ./txt/cord-010536-9ea7vvsz.txt
cache: ./cache/cord-010536-9ea7vvsz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194653/
doi: 10.1016/j.jinf.2020.03.023
abstract: nan
summary:
  The authors performed a retrospective multi-center cohort study and presented important data regarding the observation that most patients of 2019 novel coronavirus disease (COVID-19) from Wenzhou city, Zhejiang, exhibited mild infection. No study to date has provided evidence that the clinical features of critically ill patients with confirmed COVID-19 from Zhejiang province. We performed a single-centered, retrospective, observational study to investigate the clinical characteristics and ventilation conditions of critically ill patients infected with SARS-CoV-2. From late January, 2020, to February 23, 2020, 33 critically ill patients in the ICU of the First Affiliated Hospital of Zhejiang University who were diagnosed as COVID-19 in accordance with the diagnosis and treatment guidance published by the Chinese government were enrolled in the study2. The baseline epidemiological characteristics and clinical features of 33 studied patients as classified by with or without ECMO treatment, were shown in Table 1 .

title:
  Clinical characteristics and imaging manifestations of the 2019 novel coronavirus disease (COVID-19): A multi-center study in Wenzhou city, Zhejiang, China


id: cord-010540-0zkc5w74
title: Multiple parameters required for diagnosis of COVID-19 in clinical practice
author: Lei, Pinggui
date: 2020-03-19
txt: ./txt/cord-010540-0zkc5w74.txt
cache: ./cache/cord-010540-0zkc5w74.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194939/
doi: 10.1016/j.jinf.2020.03.016
abstract: nan
summary:
  We read with interest the recent papers in this Journal by Hao who described clinical features of atypical 2019 novel coronavirus pneumonia with an initially negative RT-PCR assay. 3-6 Therefore, even though chest CT plays a key role in detection or diagnosis of COVID-19 infection, however, chest CT examination and RT-PCR results should be mutual verification for precise diagnosis in the patient suspected COVID-19 infection. In conclusion, even though chest CT has played a key role in detection or diagnosis of COVID-19 infection with some typical CT features while the initial RT-PCR result is negative. However, not all the cases had the initial abnormality chest CT results or positive RT-PCR in the patients with COVID-19 infection. Consequently, RT-PCR results, chest CT features, clinical manifestation, laboratory results, and exposure history should be made a comprehensive analysis to diagnose COVID-19 infection for the clinical decisions beyond clinical and radiological features. Clinical features of atypical 2019 novel coronavirus pneumonia with an initially negative RT-PCR assay


id: cord-019964-9leljj8j
title: Recent research in infectious disease
author: nan
date: 2005-01-22
txt: ./txt/cord-019964-9leljj8j.txt
cache: ./cache/cord-019964-9leljj8j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133612/
doi: 10.1016/j.jinf.2004.11.005
abstract: nan
summary:
  These patients had significantly longer hospital stays (mean, 27.2 versus 19.4 days) and a higher risk of having Clostridium difficile-associated diarrhoea (8.3% versus 1.9%), infection-related death (23.3% versus 13.6%), and all-cause mortality (30.8% versus 19.4%) than patients whose empiric therapy was appropriate. Data were available from three endocervical swabs and a urine specimen collected from each of 1,412 women and tested by three different NAATs. Results from all three assays were used equally in a rotating fashion to define the infected-patient gold standard. Multiple different infectedpatient gold standards for estimating swab and urine specimen sensitivity and specificity for one NAAT method were created by varying the number and combinations of swab and urine comparator results with two different NAATs, The effect of changing the infected-patient gold standard definition was determined by constructing receiver-operator-like curves with calculated sensitivities and specificities for each test. LOUIS (MD Consult)-Some studies suggest antiretroviral therapy is a risk factor for gynecomastia in men with human immunodeficiency virus (HIV) infection.


id: cord-019968-o5bdb37q
title: Gastroenteritis in Auckland: An aetiological and clinical study
author: Goldwater, Paul N.
date: 2005-04-14
txt: ./txt/cord-019968-o5bdb37q.txt
cache: ./cache/cord-019968-o5bdb37q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133635/
doi: 10.1016/s0163-4453(79)90677-7
summary:
  Faecal specimens from 60 patients (under six years old), most of whom were Maoris and Pacific Islanders admitted to Auckland Hospital with gastroenteritis during the months of June and July 1977, were examined for the presence of faecal viruses, bacterial pathogens and parasites. Non-agglutinable rotavirus, presumably a different serotype, was seen in both gastroenteritis and control patients. In June and July, 1977 , patients admitted to Auckland Hospital with gastroenteritis were studied to determine the relative isolation rates of (1) rotavirus, (2) other viruses identifiable by electronmicroscopy of stools, (3) enterotoxigenic Esch. Three of 18 (17 per cent) control stools contained rotavirus (one of which had non-agglutinable virus detectable on IEM). From Table III it is seen that enterotoxigenic isolates were found in both groups of gastroenteritis patients and also in non-diarrhoeal controls. Rotavirus-like particles that failed to agglutinate on IEM were seen in two gastroenteritis patients'' stools and in one control patient''s stool.

abstract:
  Faecal specimens from 60 patients (under six years old), most of whom were Maoris and Pacific Islanders admitted to Auckland Hospital with gastroenteritis during the months of June and July 1977, were examined for the presence of faecal viruses, bacterial pathogens and parasites. Faecal specimens from 18 non-diarrhoeal control patients were also examined, of which three contained rotavirus. Forty-three (72 per cent) gastroenteritis patients had rotavirus detectable in stools by electron microscopy or immune electron microscopy. Of the remainder, 17 patients were regarded as having non-rotavirus diarrhoea. Enterotoxigenic Esch. coli. was isolated from seven patients of whom six yielded stable toxin producers (ST+), four labile toxin producers (LT+) and two dual toxigenic strains (ST+/LT+). All ST+ isolates appeared to be of low enterotoxigenicity as indicated by low gut weight/carcass weight ratios in the infant mouse assay. Rotavirus was the commonest aetiological agent (72 per cent), bacterial pathogens (alone) accounted for only five per cent and no enteric pathogens were found in 15 per cent of cases. Non-agglutinable rotavirus, presumably a different serotype, was seen in both gastroenteritis and control patients. Rotavirus ‘satellite’ particles previously undescribed were demonstrated in a number of stool samples.


id: cord-019977-kj0eaw6v
title: Neonatal bacterial infection: A changing scene?
author: nan
date: 2005-04-14
txt: ./txt/cord-019977-kj0eaw6v.txt
cache: ./cache/cord-019977-kj0eaw6v.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133668/
doi: 10.1016/s0163-4453(82)91569-9
abstract: nan
summary:
  This time period coincided with the entry of paediatricians to newborn nurseries on a much larger scale than hitherto, with an increase in the use of antimicrobial drugs, and with the introduction of apparatus such as incubators, resuscitation and suction units, the humidification parts of which often harboured Gramnegative organisms, all capable of causing lethal disease in the infant. During the half century under review, mortality from neonatal bacteraemia fell from 9o per cent in the period I928-I933, ~ to z6 per cent in I966-I978 ;6 and the proportion of isolates recorded as recovered in the first 48 hours of life (early infections) increased from IO per cent to 57 per cent of the total respectively. 16 Clostridium difficile and its toxin may be present in the stools of many well newborn babies, but this organism has not been implicated in the genesis of neonatal necrotising enterocolitis as it has been with pseudomembranous colitis.


id: cord-019982-hyxrgamj
title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles
author: Brookfield, D.S.K.
date: 2005-04-14
txt: ./txt/cord-019982-hyxrgamj.txt
cache: ./cache/cord-019982-hyxrgamj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133693/
doi: 10.1016/s0163-4453(79)91285-4
summary:
  authors: Brookfield, D.S.K.; Cosgrove, B.P.; Bell, E.J.; Madeley, C.R. title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles Causes of diarrhoea with particular reference to viral agents were investigated in 123 infants and young children in Dar es Salaam, Tanzania. The pattern of virus infection causing infantile diarrhoea was similar in Dar es Salaam to other parts of the world. The present study attempted to investigate the viruses associated with diarrhoea in Dares Salaam and, since electron microscopy was considered essential, the study was limited to the number of stools that could be sent in one consignment by air to Scotland. Examination of stools from 26 cases of measles failed to implicate any particular virus as a likely cause of the associated diarrhoea. However the diarrhoea associated with measles in Tanzanian children does not appear to be caused by any of the electron microscopically detectable viruses.

abstract:
  Causes of diarrhoea with particular reference to viral agents were investigated in 123 infants and young children in Dar es Salaam, Tanzania. Twenty-six of the patients also had measles. Viruses were found in 52 of the 123 patients (43 per cent) and rotavirus occurred in 38 children (31 per cent). Enteroviruses were found in 10 patients, adenoviruses in nine and ‘small round virus’ in one (six patients had dual infection). Four patients died and only one of these children had viral particles in the stools. Breast milk formed part or all of the diet in 77 children (63 per cent) and virus isolation showed a similar pattern in breast fed infants and those not receiving breast milk. In 26 patients with measles only five were excreting viruses in their stools. Therefore no strong evidence was found to link the diarrhoea associated with measles in Tanzanian children to any particular virus. The pattern of virus infection causing infantile diarrhoea was similar in Dar es Salaam to other parts of the world.


id: cord-025481-ljs80v45
author: Hu, Jianhua
date: 2020-05-28
txt: ./txt/cord-025481-ljs80v45.txt
cache: ./cache/cord-025481-ljs80v45.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255723/
doi: 10.1016/j.jinf.2020.05.056
abstract: nan
summary:
  Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); Coronavirus disease 2019 (COVID-19); Hypertention; Angiotensin-converting enzyme inhibitor (ACEI); Angiotensin receptor blocker (ARB); Outcome A number of pneumonia cases of unknown causes have emerged in Wuhan, Hubei, China since December 2019. Whether patients with hypertension who undergo angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB) therapy are more likely to suffer SARS-CoV-2 infection and whether ACEI/ARB therapy would have an influence on the clinical outcomes of patients with COVID-19 are controversy. Compared with patients without hypertension, patients with hypertension had a higher incidence of acute respiratory distress syndrome(ARDS) (24.16% vs 6.67%, P=0.000), were more likely to use glucocorticoids (31.54% vs 12.79%, P=0.000), antibiotic (50.33% vs 39.32%, P=0.013), and intravenous immune globulin therapy (21.48% vs 6.67%, P=0.000) and more likely to need mechanical ventilation (14.77% vs 2.04%, P=0.000) and intensive care unit (ICU) admission (16.11% vs 2.31%, P=0.000), extracorporeal membrane oxygenation (ECMO) (4.03% vs 0.82%, P=0.007) and continuous renal replacement therapy (CRRT) (2.01%vs 0.14%, P=0.016) therapy.

title:
  COVID-19 patients with hypertension have more severity condition, and ACEI/ARB treatment have no infulence on the clinical severity and outcome


id: cord-026603-h4zy3244
author: Gallo, Oreste
date: 2020-06-10
txt: ./txt/cord-026603-h4zy3244.txt
cache: ./cache/cord-026603-h4zy3244.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7286269/
doi: 10.1016/j.jinf.2020.06.011
abstract: nan
summary:
  [1] The official death toll of the COVID-19 pandemic has reached, as of May 27th, 350 000 and it is now recognised that severe outcomes of this infection are associated to a complex dysregulated immune response to SARS-CoV-2 which clinically translates into acute respiratory distress syndrome, the cytokine release syndrome, the secondary hemophagocytic lymphohistiocytosis, and the disseminated intravascular coagulation. [5] On the contrary, other authors have subsequently suggested that cancer patients, because of their impaired immune system due to the tumour itself and its therapies, are expected to have a reduced systemic inflammatory response to the virus and, thus, non-inferior mortality rates. [8] Overall, our findings seem to confirm the role of age as one of the strongest prognostic factors; in addition, we suggest that cancer patients are not necessarily at higher risk for COVID-19 associated death because their impaired immune responsiveness might act as a protective factor from the cytokine storm.

title:
  “Is really the cancer population at risk for more severe COVID-19? Some hints from the cytokine profile”


id: cord-027498-cfzfgzqi
title: Older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples
author: Hattori, Takeshi
date: 2020-06-21
txt: ./txt/cord-027498-cfzfgzqi.txt
cache: ./cache/cord-027498-cfzfgzqi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306199/
doi: 10.1016/j.jinf.2020.06.046
abstract: nan
summary:
  Currently, the standard for diagnosis of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARSinfection is a positive result based on a polymerase chain reaction (PCR) test from nasopharyngeal swab samples. Although her clinical symptoms and radiological findings resolved within a few days, PCR results from nasopharyngeal swab samples remained positive for 50 days after the onset. We specifically hypothesized that old age could be a risk for prolonged duration of positive PCR results from nasopharyngeal swab samples. In our analysis, older age is significantly associated with prolonged duration of positive PCR tests from nasopharyngeal swab samples, irrespective of the disease severity and the used of medication ( Figure 1 ). In summary, we demonstrated that old age is significantly associated with prolonged duration of positive PCR results from nasopharyngeal swab samples; this is the case regardless of disease severity.


id: cord-030594-xhp8kin0
title: Dear the Editor,
author: nan
date: 2020-08-19
txt: ./txt/cord-030594-xhp8kin0.txt
cache: ./cache/cord-030594-xhp8kin0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7434637/
doi: 10.1016/j.jinf.2020.08.021
abstract: nan
summary:
  have written to this journal regarding elevated admission levels of markers of liver injury (alanine aminotransferase and aspartate aminotransferase, gamma-glutamyltransferase, alkaline phosphatase and total bilirubin) may be associated with progression to severe disease or death in COVID-19. In critically ill patients with favorable outcome, cholinesterase, lymphocytes, albumin, and PaO 2 /FiO 2 ratio decreased but C-reactive protein increased toward the peak of inflammation. Later, C-reactive protein decreased with improvement in inflammation, but there was a tendency for cholinesterase, lymphocytes, albumin, and PaO 2 /FiO 2 ratio to increase. In contrast, in the severely ill patient who died, C-reactive protein poorly decreased, and cholinesterase, lymphocytes, albumin, and PaO 2 /FiO 2 ratio were not elevated. [4] Our study suggests that cholinesterase, which responds similar to the "negative" acute-phase proteins in response to inflammation, is reduced even in the acute phase of severe COVID-19 pneumonia.


id: cord-030636-wpjmwwpu
title: Dear Editor,
author: nan
date: 2020-08-19
txt: ./txt/cord-030636-wpjmwwpu.txt
cache: ./cache/cord-030636-wpjmwwpu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7437568/
doi: 10.1016/j.jinf.2020.08.023
abstract: nan
summary:
  authors: nan Despite the observation that elderly subjects are more susceptible to severe illness, probably due to underlying co-morbidities such as diabetes, hypertension, cardiovascular and cerebro-vascular diseases, 1,2 literature concerning geriatric patients with COVID-19 pneumonia remained very scant. We included in this analysis 118 consecutive patients; data on clinical and demographic characteristics, blood test results and COVID-19-related treatments were collected. Elderly patients have higher levels of inflammatory blood tests at the time of admission in the emergency department; in particular, elevated d-dimer levels was an independent predictor of mortality, confirming the close correlation between this parameter and the severity of COVID-19 disease. In conclusion, our study confirms that the majority of elderly subjects with COVID-19 pneumonia have an unfavorable outcome, especially in the very first days after admission. Analysis of epidemiological and clinical features in older patients with coronavirus disease 2019 (COVID-19) outside Wuhan


id: cord-252980-1e28zj1d
title: Insights into the cross-species evolution of 2019 novel coronavirus
author: Zhang, Jiahao
date: 2020-03-04
txt: ./txt/cord-252980-1e28zj1d.txt
cache: ./cache/cord-252980-1e28zj1d.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320301067
doi: 10.1016/j.jinf.2020.02.025
abstract: nan
summary:
  5 Although humans and bats live in different environments, some wildlife species were susceptible to the novel coronaviruses in nature, highlighting that the need of tracing its origin of SARS-CoV-2 in wild animals. The similarity analysis of SARS-CoV-2 and the animal-origin coronaviruses demonstrated that recombination events were likely to occur in bat-and pangolin-origin coronaviruses (Supplementary Figure S1) . Although the S amino acid identities of pangolin-origin coronavirus exhibited lower amino acid identities with bat/RaTG13, it was noteworthy that six amino acids associated with the receptor binding preference of human receptor angiotensin converting enzyme II-464 L, 495F, 502Q, 503S, 510 N, and 514Y (SARS-CoV-2 numbering)-in the pangolin/1 coronavirus were the same as that of SARS-CoV-2 ( Fig. 2 ), but were distinct from that of the bat-origin coronaviruses. Besides, the PRRA-motif insertion was occurred in the S1/S2 junction of SARS-CoV-2; however, the PRRA-motif insertion in the pangolin-and bat-origin coronaviruses was missing (Supplementary Figure S4 ), suggesting that the convergent cross-species evolution of SARS-CoV-2-related coronaviruses. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus


id: cord-254512-dct045kl
title: Imported COVID-19 Cases Pose New Challenges for China
author: Chen, Libin
date: 2020-04-10
txt: ./txt/cord-254512-dct045kl.txt
cache: ./cache/cord-254512-dct045kl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32283157/
doi: 10.1016/j.jinf.2020.03.048
abstract: nan
summary:
  Libin Chen a,b,c,d , Juncheng Cai a,b,c,d , Qiuyan Lin a,b,c,d , Bin Xiang a,b,c,d* ,and Tao That translates to a mortality rate of 9.51%, which is more than twice as high as that For China-the initial epicenter of the outbreak-two stages of the epidemic have passed ( Figure 1A ). Therefore, the conundrum regarding the control over overseas imported cases as well as the prevention of a second epidemic outbreak that is fast approaching is a problem that China needs to pay special attention to, especially after the first second-generation case imported from abroad had appeared. However, due to the lack of attention and the spread of misinformation regarding COVID-19 in many countries, the disease has seriously threatened the whole world 4 , bringing China''s epidemic to the third stage. Three stages of China''s COVID-19 epidemic The first and second stages of China''s COVID-19 epidemic.


id: cord-254556-1zthrgy1
author: Taylor, Sylvia
date: 2016-09-22
txt: ./txt/cord-254556-1zthrgy1.txt
cache: ./cache/cord-254556-1zthrgy1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27667752/
doi: 10.1016/j.jinf.2016.09.003
summary:
  METHODS: The epidemiology of respiratory viruses among healthy children (6 months to <10 years) with influenza-like illness (ILI) was determined in a population sample derived from an influenza vaccine trial (NCT01051661) in 17 centers in eight countries (Australia, South East Asia and Latin America). As part of a trial of pandemic influenza vaccines, which included 1 year of prospective, active, community-based surveillance for influenza-like illness (ILI) in 17 centers in eight countries, 8 we evaluated the prevalence and incidence of respiratory viruses in children 6 months to less than 10 years of age at first vaccination. Rhinovirus/enterovirus had the highest prevalence and incidence in ILI of all respiratory viruses tested in all countries, followed by influenza, adenovirus, parainfluenza and RSV, coronavirus, hMPV and HBov. The burden of ILI associated with respiratory viruses was considerable, with a high proportion of children being seen by a medical professional and many missing school or daycare.

title:
  Respiratory viruses and influenza-like illness: Epidemiology and outcomes in children aged 6 months to 10 years in a multi-country population sample

abstract:
  BACKGROUND: Better population data on respiratory viruses in children in tropical and southern hemisphere countries is needed. METHODS: The epidemiology of respiratory viruses among healthy children (6 months to <10 years) with influenza-like illness (ILI) was determined in a population sample derived from an influenza vaccine trial (NCT01051661) in 17 centers in eight countries (Australia, South East Asia and Latin America). Active surveillance for ILI was conducted for approximately 1 year (between February 2010 and August 2011), with PCR analysis of nasal and throat swabs. RESULTS: 6266 children were included, of whom 2421 experienced 3717 ILI episodes. Rhinovirus/enterovirus had the highest prevalence (41.5%), followed by influenza (15.8%), adenovirus (9.8%), parainfluenza and respiratory syncytial virus (RSV) (both 9.7%), coronavirus (5.6%), human metapneumovirus (5.5%) and human bocavirus (HBov) (2.0%). Corresponding incidence per 100 person-years was 29.78, 11.34, 7.03, 6.96, 6.94, 4.00, 3.98 and 1.41. Except for influenza, respiratory virus prevalence declined with age. The incidence of medically-attended ILI associated with viral infection ranged from 1.03 (HBov) to 23.69 (rhinovirus/enterovirus). The percentage of children missing school or daycare ranged from 21.4% (HBov) to 52.1% (influenza). CONCLUSIONS: Active surveillance of healthy children provided evidence of respiratory illness burden associated with several viruses, with a substantial burden in older children.


id: cord-254635-gtgahlqm
author: Sun, Guanghao
date: 2014-12-23
txt: ./txt/cord-254635-gtgahlqm.txt
cache: ./cache/cord-254635-gtgahlqm.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445314003788
doi: 10.1016/j.jinf.2014.12.007
summary:
  title: An infectious disease/fever screening radar system which stratifies higher-risk patients within ten seconds using a neural network and the fuzzy grouping method METHODS: The system screens infected patients based on vital signs, i.e., respiration rate measured by a radar, heart rate by a finger-tip photo-reflector, and facial temperature by a thermography. 9 Considering the defective fever screening method, we previously developed a noncontact screening system for performing medical examinations within 10 s using measured vital signs (i.e. heart rate, respiration rate, and facial temperature). ''0 Z Non-influenza'', ''1 Z Lower-risk influenza'', or ''2 Z Higher-risk influenza'') are obtained by the neural network and fuzzy clustering algorithm, based on the derived multiple vital signs (Fig. 2) . 13 More importantly, the proposed optimal neural network and fuzzy clustering method were used to classify the multiple-dimensional vital-sign data to detect higher-risk influenza patients.

title:
  An infectious disease/fever screening radar system which stratifies higher-risk patients within ten seconds using a neural network and the fuzzy grouping method

abstract:
  OBJECTIVES: To classify higher-risk influenza patients within 10 s, we developed an infectious disease and fever screening radar system. METHODS: The system screens infected patients based on vital signs, i.e., respiration rate measured by a radar, heart rate by a finger-tip photo-reflector, and facial temperature by a thermography. The system segregates subjects into higher-risk influenza (HR-I) group, lower-risk influenza (LR-I) group, and non-influenza (Non-I) group using a neural network and fuzzy clustering method (FCM). We conducted influenza screening for 35 seasonal influenza patients and 48 normal control subjects at the Japan Self-Defense Force Central Hospital. Pulse oximetry oxygen saturation (SpO(2)) was measured as a reference. RESULTS: The system classified 17 subjects into HR-I group, 26 into LR-I group, and 40 into Non-I group. Ten out of the 17 HR-I subjects indicated SpO(2) <96%, whereas only two out of the 26 LR-I subjects showed SpO(2) <96%. The chi-squared test revealed a significant difference in the ratio of subjects showed SpO(2) <96% between HR-I and LR-I group (p < 0.001). There were zero and nine normal control subjects in HR-I and LR-I groups, respectively, and there was one influenza patient in Non-I group. CONCLUSIONS: The combination of neural network and FCM achieved efficient detection of higher-risk influenza patients who indicated SpO(2) 96% within 10 s.


id: cord-255174-h1izji2g
title: Risk factors for severe COVID-19: evidence from 167 hospitalized patients in Anhui, China
author: Wei, Yuan-Yuan
date: 2020-04-17
txt: ./txt/cord-255174-h1izji2g.txt
cache: ./cache/cord-255174-h1izji2g.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S016344532030219X?v=s5
doi: 10.1016/j.jinf.2020.04.010
abstract: nan
summary:
  It is very important to analyse the clinical characteristics of COVID-19 in international regions and identify risk factors to reduce the incidence of severe and critical illness in the early stage. In this letter, we present discrepancies of patients with different disease severities and risk factors for severe COVID-19 by comparing and analysing epidemiological and clinical data of 167 confirmed patients in Anhui, China. There are still no specific therapies for COVID-19(1); nevertheless, assessing risk factors and symptomatic treatment in the early stage of the disease can improve the prognosis. The similarities and differences between severe and non-severe patients in this letter suggested that elderly patients with multiple comorbidities, hypoxia, decreased CD4 and CD8 cell counts and increased levels of CRP and IL-6 are all closely associated with disease severity and prognosis, which should be assessed seriously during diagnosis and treatment. MDT consultation and artificial liver therapy are very effective methods for severe patients with COVID-19.


id: cord-256633-vls23fu5
title: The SARS-CoV-2 seroprevalence is the key factor for deconfinement in France
author: Dimeglio, Chloé
date: 2020-04-29
txt: ./txt/cord-256633-vls23fu5.txt
cache: ./cache/cord-256633-vls23fu5.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320302425
doi: 10.1016/j.jinf.2020.04.031
summary:
  We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. Our statistical model for predicting the spread of SARS-CoV-2 in France is based on a diffusion and transmission coefficient that varies with an individual''s age, the likelihood of contagion, and two administration parameters (confinement and quarantine). Figures 1.b, 1 .c, 1.d, 1.e showed predictions of new cases per day depending on the SARS-CoV-2 seroprevalence before and after the containment phase. Our data indicate that seroprevalence must reach approximately 50% after total deconfinement on May 11 or a gradual exit phase over several months starting on May 11 if an infection rebound is to be avoided (Figure 1 .d, 1.e and Figure 2 .b).

abstract:
  A new virus, SARS-CoV-2, has spread world-wide since December 2019, probably affecting millions of people and killing thousands. Failure to anticipate the spread of the virus now seriously threatens many health systems. We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy.


id: cord-256808-lxlerb13
author: Lim, W.S
date: 2004-06-02
txt: ./txt/cord-256808-lxlerb13.txt
cache: ./cache/cord-256808-lxlerb13.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445304000830
doi: 10.1016/j.jinf.2004.04.001
summary:
  Severe Acute Respiratory Syndrome (SARS) is a potentially severe and highly infectious disease to which healthcare workers involved in the management of cases are particularly vulnerable. These guidelines briefly summarise optimal and safe practice for clinicians involved in the emergency care of patients with probable or confirmed SARS. During 2003 Severe Acute Respiratory Syndrome caused by a novel coronavirus (SARS-CoV) emerged as an infectious disease with a significant inhospital mortality and posed a considerable occupational risk for healthcare workers. Please discuss the classification of SARS patients with the Health Protection Agency''s Communicable Disease Surveillance Centre (CDSC) Duty doctor (Tel.: 0208-200-6868) and complete a standard SARS report form and fax to your local Consultant in Communicable Disease Control (CCDC) and CDSC (details at: http://www.hpa.org.uk/infections/ topics_az/SARS/forms.htm). Inform the local Health Protection Team/CCDC regarding the hospital discharge of patients to ensure follow-up in the community. Severe acute respiratory syndrome (SARS): infection control

title:
  Hospital management of adults with severe acute respiratory syndrome (SARS) if SARS re-emerges—updated 10 February 2004

abstract:
  Severe Acute Respiratory Syndrome (SARS) is a potentially severe and highly infectious disease to which healthcare workers involved in the management of cases are particularly vulnerable. These guidelines briefly summarise optimal and safe practice for clinicians involved in the emergency care of patients with probable or confirmed SARS.


id: cord-257489-ruf4rzxm
title: Influenza vaccine coverage rates and perceptions on vaccination in South Korea
author: Kee, Sae Yoon
date: 2007-06-28
url: https://www.sciencedirect.com/science/article/pii/S0163445307006287
doi: 10.1016/j.jinf.2007.04.354
abstract:
  OBJECTIVE: This survey was performed to assess the level of influenza vaccine coverage, to understand the driving forces and barriers to vaccination and determine vaccination interventions for the following year in Korean population. METHODS: A national sample of 1720 community dwelling adults of age 18 and older were surveyed by individual visits during April 2005. Demographics, state of influenza vaccination, reasons for vaccination or non-vaccination and perceptions on vaccinations were asked by questionnaire. RESULTS: Influenza vaccination coverage in general population and high risk group was 34.3% and 61.3%, respectively. Predictors for vaccination were ≥65 of age, performance of regular exercise, vaccination in the previous season, experience of influenza-like illness, belief that vaccine can prevent common cold and opinion that vaccine must be taken annually. The most common reason for vaccination for both whole population and high risk groups was to prevent both influenza and common cold, while the most common reason for non-vaccination was the thought that he/she was healthy enough not to be in need for vaccination. Having more information on influenza and vaccination as well as doctor's recommendation for vaccination appeared to be the most important modus operandi to encourage influenza vaccination among non-vaccinees. CONCLUSIONS: Doctor's recommendation was the most important factor in encouraging people to be vaccinated against influenza. Doctors should be geared up with precise information and actively encourage high risk population in order to increase vaccination coverage.


id: cord-257732-3xuy6tbn
title: Saliva is a reliable tool to detect SARS-CoV-2
author: Azzi, Lorenzo
date: 2020-04-14
txt: ./txt/cord-257732-3xuy6tbn.txt
cache: ./cache/cord-257732-3xuy6tbn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32298676/
doi: 10.1016/j.jinf.2020.04.005
summary:
  OBJECTIVES: This study analyzed salivary samples of COVID-19 patients and compared the results with their clinical and laboratory data. At present, Real Time reverse transcription Polymerase Chain Reaction (rRT-PCR) on respiratory specimens represents the gold standard test for detection of SARS-CoV-2 infection. 10 , 11 Sputum and oropharyngeal secretions have recently been suggested as a possible target for the molecular diagnosis of COVID-19, 12 and salivary droplets represent the main source of the human-to-human transmission of the SARS-CoV-2 infection when social distance is less than 2 m. There were not significant differences regarding the clinical and anamnestic history between males and females, with the only exception of the values of serum LDH, which were higher in the female patients'' haematochemical analyses carried out on the day of saliva collection ( p = 0.025).

abstract:
  OBJECTIVES: This study analyzed salivary samples of COVID-19 patients and compared the results with their clinical and laboratory data. METHODS: Salivary samples of 25 COVID-19 patients were analyzed by rRT-PCR. The following data were collected: age, sex, comorbidities, drugs. Lactate dehydrogenase (LDH) and ultrasensitive reactive C protein (usRCP) values were registered on the same day when a salivary swab was collected. Prevalence of positivity in saliva and association between clinical data and the cycle threshold as a semiquantitative indicator of viral load were considered. RESULTS: Twenty-five subjects were recruited into this study, 17 males and 8 females. The mean age was 61.5 +/− 11.2 years. Cardiovascular and/or dysmetabolic disorders were observed in 65.22% of cases. All the samples tested positive for the presence of SARS-CoV-2, while there was an inverse association between LDH and Ct values. Two patients showed positive salivary results on the same days when their pharyngeal or respiratory swabs showed conversion. CONCLUSIONS: Saliva is a reliable tool to detect SARS-CoV-2. The role of saliva in COVID-19 diagnosis could not be limited to a qualitative detection of the virus, but it may also provide information about the clinical evolution of the disease.


id: cord-260247-akujsk0s
title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar
author: Hamed, Ehab
date: 2020-11-02
txt: ./txt/cord-260247-akujsk0s.txt
cache: ./cache/cord-260247-akujsk0s.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320306915
doi: 10.1016/j.jinf.2020.10.029
abstract: nan
summary:
  title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar The group suggested recurrent positive rt-PCR results of more than 21 days following the resolution of symptoms as criteria for reinfection. Utilising the criteria set by the COCOREC study group, this record-based study reports on the cases with recurrent positive RT-PCR nasopharyngeal swab for SARS-CoV-2 results in primary health care corporation (PHCC) settings in Qatar. The study population included patients attending with documented SARS-CoV-2 rt-PCR results during the study period. What are the rates of recurrent rt-PCR SARS-CoV-2 positive results of more than 21 days, and what are the population characteristics? No previous studies reported to the rates of recurrent positive rt-PCR for SARS-CoV-2 infections. Given the extensive reporting of the SARS-CoV-2 infections, the number of case reports of recurrent positive and reinfection to date is extremely low, which agrees with our findings.


id: cord-260925-puuqv6zk
title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2
author: Wen, Feng
date: 2020-03-05
txt: ./txt/cord-260925-puuqv6zk.txt
cache: ./cache/cord-260925-puuqv6zk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.02.027
doi: 10.1016/j.jinf.2020.02.027
abstract: nan
summary:
  title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 The sequences NC_004718.3 of SARS coronavirus 6 genes were utilized to define the protein products of SARS-CoV-2. First, the protein sequences of SARS-CoV-2 were compared with RaTG13, human SARS (NC_004718.3), bat SARS (DQ022305.2), and human MERS (NC_019843.3) by calculating the similarity in a given sliding window ( Fig. 1 A) . These results suggested that there had probably been no hyper-variable genomic hotspot in the SARS-CoV-2 population until now. The hyper-variable genomic hotspot has been established in the SARS-CoV-2 population at the nucleotide but not the amino acid level, suggesting that there have been no beneficial mutations. mutations in nsp1, nsp3, nsp15, and gene S that identified in this study would be associated with the SARS-CoV-2 epidemic and was worthy of further study. The genome sequence of the SARS-associated coronavirus


id: cord-261240-osbk041e
title: Lymphopenic community acquired pneumonia as signature of severe COVID-19 infection
author: Bermejo-Martin, Jesús F
date: 2020-03-05
txt: ./txt/cord-261240-osbk041e.txt
cache: ./cache/cord-261240-osbk041e.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320301109
doi: 10.1016/j.jinf.2020.02.029
abstract: nan
summary:
  The presence of lymphopenia as a signature of severe COVID-19 was confirmed by Wang D et al., who, in their study published in JAMA, reported that ICU patients suffering this infection had a median lymphocyte count of 800 cells/mm [3] , with non survivors exhibiting persistent lymphopenia [4] . Interestingly, hypercytokinemia and lymphopenia were also evident in critical patients with Severe Acute Respiratory Syndrome due to the Coronavirus emerged in 2003 (SARS-CoV) [5 , 6] . These features (lymphopenia + hypercytokinemia) fit the characteristics of a particular immunological phenotype of community acquired pneumonia (CAP), lymphopenic CAP (L-CAP), which, as we recently demonstrated in an article published in the Journal of Infection, is associated with increased severity, mortality and a dysregulated immunological response [7] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China


id: cord-261405-n05wjimk
title: Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19
author: Lui, Grace
date: 2020-04-18
txt: ./txt/cord-261405-n05wjimk.txt
cache: ./cache/cord-261405-n05wjimk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.04.014
doi: 10.1016/j.jinf.2020.04.014
abstract: nan
summary:
  reported in this journal that viral shedding of SARS-CoV-2 in nasal swabs was longer in intensive care unit (ICU) patients compared with non-ICU patients with Coronavirus Disease 2019 (COVID-19). 3 We collected serial upper (pooled nasopharyngeal and throat swabs, N=75) and lower respiratory tract samples (sputum and tracheal aspirate, N=43), peripheral blood plasma (N=50), urine (N=43) and stool (N=43) samples from all participants, and monitored SARS-CoV-2 viral loads in these samples. In all five participants with severe/critical and three with moderate disease, viral loads in respiratory tract samples continued to rise and peaked in the second week of illness (range 5.57-9.66 log copies/mL). In this study of patients with COVID-19 across a wide spectrum of severity, we observed that viral shedding in the respiratory tract lasting longer than 14 days was common. In more severe disease, viral load appeared to peak in the second week of illness in both upper and lower respiratory tract.


id: cord-263671-2b54qfo7
author: Soriano, María Cruz
date: 2020-09-19
txt: ./txt/cord-263671-2b54qfo7.txt
cache: ./cache/cord-263671-2b54qfo7.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320305946
doi: 10.1016/j.jinf.2020.09.010
abstract: nan
summary:
  title: Low incidence of co-infection, but high incidence of ICU-acquired infections in critically ill patients with COVID-19 ICU admission is a risk factor for hospital-acquired infections and nosocomial infections by multidrug-resistant (MDR) bacteria 2, 3 . Here, we report our findings of a retrospective cohort study to asses the incidence of co-infections, ICU-acquired infections and their relation to mortality in patients with COVID-19. Frequency measurements have been calculated using the incidence rates of each ICU-acquired infections expressed in relation to the number of patients at risk or the number of days at risk. A study conducted in Wuhan, China shows a series of 150 hospitalized COVID-19 patients in whom the presence of secondary infection during hospital admission was one of the risk factors for increased mortality 5 . A recent study found that frequency of hospital-acquired superinfections remained low and this finding was mainly related with ICU admission 6 .

title:
  Low incidence of co-infection, but high incidence of ICU-acquired infections in critically ill patients with COVID-19


id: cord-264255-q5izs39f
author: Chieochansin, Thaweesak
date: 2007-12-31
txt: ./txt/cord-264255-q5izs39f.txt
cache: ./cache/cord-264255-q5izs39f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18164764/
doi: 10.1016/j.jinf.2007.11.006
summary:
  title: Human bocavirus (HBoV) in Thailand: Clinical manifestations in a hospitalized pediatric patient and molecular virus characterization OBJECTIVE: Human bocavirus (HBoV), a novel virus, which based on molecular analysis has been associated with respiratory tract diseases in infants and children have recently been studied worldwide. METHODS: HBoV was detected from 302 nasopharyngeal (NP) suctions of pediatric patients with acute lower respiratory tract illness and sequenced applying molecular techniques. CONCLUSION: Our results indicated that HBoV can be detected in nasopharyngeal aspirate specimens from infants and children with acute lower respiratory tract illness. Therefore, in the present study we applied polymerase chain reaction to detect HBoV from NP suctions collected from infants or children who had been admitted with respiratory tract illness. Detection of human bocavirus in Japanese children with lower respiratory tract infection Human bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection

title:
  Human bocavirus (HBoV) in Thailand: Clinical manifestations in a hospitalized pediatric patient and molecular virus characterization

abstract:
  OBJECTIVE: Human bocavirus (HBoV), a novel virus, which based on molecular analysis has been associated with respiratory tract diseases in infants and children have recently been studied worldwide. To determine prevalence, clinical features and perform phylogenetic analysis in HBoV infected Thai pediatric patients. METHODS: HBoV was detected from 302 nasopharyngeal (NP) suctions of pediatric patients with acute lower respiratory tract illness and sequenced applying molecular techniques. RESULTS: The incidence of HBoV infection in pediatric patients amounted to 6.62% with 40% co-infected with other respiratory viruses. There were no clinical specific manifestations for HBoV; however, fever and productive cough were commonly found. Generalized rales and wheezing were detected in most of the patients as well as perihilar infiltrates. The alignment and phylogenetic analysis of partial VP1 genes showed minor variations. CONCLUSION: Our results indicated that HBoV can be detected in nasopharyngeal aspirate specimens from infants and children with acute lower respiratory tract illness.


id: cord-264285-1sne3ng1
author: Sze, Shirley
date: 2020-05-29
txt: ./txt/cord-264285-1sne3ng1.txt
cache: ./cache/cord-264285-1sne3ng1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32479770/
doi: 10.1016/j.jinf.2020.05.063
summary:
  title: Letter to the Editor: Variability but not admission or trends in NEWS2 score predicts clinical outcome in elderly hospitalised patients with COVID-19 (4) Compared to other early warning scores, the NEWS Score has a greater ability to discriminate patients at risk of cardiac arrest, unanticipated intensive care unit admission or death. (5) Currently, guidance from the National Institute of Clinical Excellence (NICE) supports the use of the NEWS2 score to risk assess patients with COVID-19 in the community, who may require hospitalisation. Figure 1 shows the trend in the National Early Warning Score2 (NEWS2) throughout hospitalisation, stratified by severity of NEWS2 on admission and clinical outcome. In our small pilot of elderly patients admitted to hospital with COVID-19, admission NEWS2 scores did not seem to be useful in predicting clinical outcomes. The ability of the National Early Warning Score (NEWS) to discriminate patients at risk of early cardiac arrest, unanticipated intensive care unit admission, and death

title:
  Letter to the Editor: Variability but not admission or trends in NEWS2 score predicts clinical outcome in elderly hospitalised patients with COVID-19

abstract:
  • In elderly COVID-19 inpatients, admission NEWS2 scores did not predict mortality. • Of components of NEW2 score, only systolic blood pressure predicted mortality. • A high variability in NEW2 score predicted mortality. • NEWS2 score does not consider the degree of supplemental oxygen patients require. • A more sensitive early warning score for COVID-19 is needed.


id: cord-264302-8vo5psgm
title: Social media WeChat infers the development trend of COVID-19
author: Lu, Yue
date: 2020-04-10
txt: ./txt/cord-264302-8vo5psgm.txt
cache: ./cache/cord-264302-8vo5psgm.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320301766
doi: 10.1016/j.jinf.2020.03.050
abstract: nan
summary:
  5 Information and discussions on COVID-19 spread rapidly on social media, so the use of big data allows more people to pay attention to these situations earlier. Here, through the keyword query in the WeChat index, we analyzed the public attention and demand for the COVID-19 pandemic. First of all, the hottest words in the pandemic are "Wuhan", "novel coronavirus" and "pneumonia" ( Fig. 1 A) . Thus, during the period from the end of January to the beginning of February, the public attention focused on those words. Through analysis of public concerns, we review the development trend of COVID-19, which will set up an example for future outbreaks of epidemic diseases. It is believed that public health authorities will rely more on these social medias in the future for monitoring the development of the epidemic or pandemic. Retrospective analysis of the possibility of predicting the COVID-19 outbreak from internet searches and social media data, China


id: cord-265504-yq9wsugy
title: Water scarcity and COVID-19 in sub-Saharan Africa
author: Anim, Desmond Ofosu
date: 2020-05-21
txt: ./txt/cord-265504-yq9wsugy.txt
cache: ./cache/cord-265504-yq9wsugy.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320303121?v=s5
doi: 10.1016/j.jinf.2020.05.032
abstract: nan
summary:
  In this paper, we highlight the issues that characterize water services amid the COVID-19 pandemic in sub-Saharan Africa (SSA) and discuss avenues for improving water management during this pandemic and future infectious disease outbreaks. In response to the promotion of hand hygiene by the World Health Organization (WHO) and national public health agencies as a means to curbing the spread of COVID-19, Water Service Providers (WSP) in most developed countries have outlined drastic measures with the goal of ensuring continuous provision of essential water and sewerage services to all during this pandemic. Nevertheless, across many SSA countries where inequalities in access to safe water is pervasive [6] , there is a need to be worried in light of COVID-19 pandemic. Ensuring affordable access to safe water, sanitation and hygiene (WASH) services is important to address the current COVID-19 and future pandemics.


id: cord-265772-diahoew3
title: Genotype shift in human coronavirus OC43 and emergence of a novel genotype by natural recombination
author: Zhang, Yue
date: 2014-12-18
txt: ./txt/cord-265772-diahoew3.txt
cache: ./cache/cord-265772-diahoew3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2014.12.005
doi: 10.1016/j.jinf.2014.12.005
summary:
  METHODS: The full-length spike (S), RNA-dependent RNA polymerase (RdRp), and nucleocapsid (N) genes were amplified from each respiratory sample collected from 65 HCoV-OC43-positive patients between 2005 and 2012. In this study, we genotyped HCoV-OC43 by analyzing fulllength sequences of S, RdRp, N genes and viral genomes directly from respiratory samples collected from 65 HCoV-OC43 positive patients with acute respiratory tract infections (ARTIs) recruited from 2005 to 2012. The nucleotide sequence data of S, RdRp, N genes and viral genomes of HCoV-OC43 used in this study have been lodged in GenBank and the accession numbers are shown in Table S2 . To genotype the HCoV-OC43 samples, we constructed ML trees using the full-length sequences of S, RdRp and N genes amplified from the 65 respiratory samples of HCoV-OC43 positive patients in this study and compared them to those retrieved from GenBank (Fig. 1) .

abstract:
  BACKGROUND: Human coronavirus (HCoV) OC43 is the most prevalent HCoV in respiratory tract infections. Its molecular epidemiological characterization, particularly the genotyping, was poorly addressed. METHODS: The full-length spike (S), RNA-dependent RNA polymerase (RdRp), and nucleocapsid (N) genes were amplified from each respiratory sample collected from 65 HCoV-OC43-positive patients between 2005 and 2012. Genotypes were determined by phylogenetic analysis. Recombination was analyzed based on full-length viral genome sequences. Clinical manifestations of each HCoV genotype infection were compared by reviewing clinical records. RESULTS: Sixty of these 65 samples belong to genotypes B, C and D. The remaining five strains had incongruent positions in the phylogenetic trees of the S, RdRp and N genes, suggesting a novel genotype emerging, designated as genotype E. Whole genome sequencing and bootscan analysis indicated that genotype E is generated by recombination between genotypes B, C and D. Temporal analysis revealed a sequential genotype replacement of C, B, D and E over the study period with genotype D being the dominant genotype since 2007. The novel genotype E was only detected in children younger than three years suffering from lower respiratory tract infections. CONCLUSIONS: Our results suggest that HCoV-OC43 genotypes are evolving. Such genotype shift may be an adapting mechanism for HCoV-OC43 maintaining its epidemic.


id: cord-266033-gbx48scp
author: Xu, Yu-Huan
date: 2020-02-25
txt: ./txt/cord-266033-gbx48scp.txt
cache: ./cache/cord-266033-gbx48scp.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320301006
doi: 10.1016/j.jinf.2020.02.017
summary:
  Based on the fifth edition of the China Guidelines for the Diagnosis and Treatment Plan of Novel Coronavirus (2019-nCoV) Infection by the National Health Commission (Trial Version 5), 6 the NCP was classified into four types: mild with slight clinical symptoms but no imaging presentations of pneumonia; common with fever, respiratory symptoms and imaging presentations of pneumonia; severe type with any of the following: respiratory distress with RR > 30 times/minutes, oxygen saturation at rest < 93%, or PaO2/FiO2 < 300 mmHg (1 mmHg = 0.133 kPa); critically severe type with any of the following: respiratory failure needing mechanical ventilation, shock, or combination with other organ failure needing ICU intensive care. Fifty patients with NCP caused by infection of the SARS-CoV-2 virus were enrolled and had high-resolution pulmonary CT scanning, including mild type in nine, common in 28, severe in 10 and critically severe in the rest three ( Table 1 ).

title:
  Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2

abstract:
  PURPOSE: To investigate the clinical and imaging characteristics of computed tomography (CT) in novel coronavirus pneumonia (NCP) caused by SARS-CoV-2. MATERIALS AND METHODS: A retrospective analysis was performed on the imaging findings of patients confirmed with COVID-19 pneumonia who had chest CT scanning and treatment after disease onset. The clinical and imaging data were analyzed. RESULTS: Fifty patients were enrolled, including mild type in nine, common in 28, severe in 10 and critically severe in the rest three. Mild patients (29 years) were significantly (P<0.03) younger than either common (44.5 years) or severe (54.7) and critically severe (65.7 years) patients, and common patients were also significantly (P<0.03) younger than severe and critically severe patients. Mild patients had low to moderate fever (<39.1 °C), 49 (98%) patients had normal or slightly reduced leukocyte count, 14 (28%) had decreased counts of lymphocytes, and 26 (52%) patients had increased C-reactive protein. Nine mild patients were negative in CT imaging. For all the other types of NCP, the lesion was in the right upper lobe in 30 cases, right middle lobe in 22, right lower lobe in 39, left upper lobe in 33 and left lower lobe in 36. The lesion was primarily located in the peripheral area under the pleura with possible extension towards the pulmonary hilum. Symmetrical lesions were seen in 26 cases and asymmetrical in 15. The density of lesion was mostly uneven with ground glass opacity as the primary presentation accompanied by partial consolidation and fibrosis. CONCLUSION: CT imaging presentations of NCP are mostly patchy ground glass opacities in the peripheral areas under the pleura with partial consolidation which will be absorbed with formation of fibrotic stripes if improved. CT scanning provides important bases for early diagnosis and treatment of NCP.


id: cord-266036-qhlo99l7
title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review
author: Axell-House, Dierdre B.
date: 2020-08-31
txt: ./txt/cord-266036-qhlo99l7.txt
cache: ./cache/cord-266036-qhlo99l7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.08.043
doi: 10.1016/j.jinf.2020.08.043
summary:
  OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations.

abstract:
  OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. METHODS: We conducted a systematic search of English-language articles published December 31, 2019-June 19, 2020. Studies of any design that performed tests on ≥10 patients and reported or inferred correlative statistics were included. Studies were evaluated using elements of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. RESULTS: We conducted a narrative and tabular synthesis of studies organized by their reference standard strategy or comparative agreement method, resulting in six categorizations. Critical study details were frequently unreported, including the mechanism for patient/sample selection and researcher blinding to results, which lead to concern for bias. CONCLUSIONS: Current studies estimating test performance characteristics have imperfect study design and statistical methods for the estimation of test performance characteristics of SARS-CoV-2 tests. The included studies employ heterogeneous methods and overall have an increased risk of bias. Employing standardized guidelines for study designs and statistical methods will improve the process for developing and validating rRT-PCR and NAAT for the diagnosis of COVID-19.


id: cord-266455-rbblg4pu
title: Rapid syndromic molecular testing in pneumonia: The current landscape and future potential
author: Poole, Stephen
date: 2019-12-03
txt: ./txt/cord-266455-rbblg4pu.txt
cache: ./cache/cord-266455-rbblg4pu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31809764/
doi: 10.1016/j.jinf.2019.11.021
summary:
  Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. This is an FDA approved and CE marked platform that uses nested real-time PCR to detect 34 clinically important respiratory targets (15 semi-quantitative bacterial targets, 3 qualitative atypical bacterial targets, 8 [30] [31] [32] Furthermore, the pneumonia panel detects pathogens in a much higher proportion of samples than culture. Rapid syndromic molecular platforms have the potential to significantly improve the use of antibiotics and clinical outcomes in patient with pneumonia, but high quality randomised controlled trials are urgently required to evaluate their clinical impact. an observational study comparing the performance of two multiplex PCR platforms against routine microbiology for the detection of potential pathogens in patients with suspected hospital acquired/ventilator associated pneumonia (HAP/VAP) across

abstract:
  Community acquired pneumonia (CAP), hospital-acquired pneumonia (HAP) and ventilator associated pneumonia (VAP) are all associated with significant mortality and cause huge expense to health care services around the world. Early, appropriate antimicrobial therapy is crucial for effective treatment. Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. In this article we review the currently available testing platforms and discuss the potential benefits and pitfalls of rapid testing in pneumonia.


id: cord-266564-imj1lcy9
title: Clinical manifestations and outcome of SARS-CoV-2 infection during pregnancy
author: Liu, Yangli
date: 2020-03-05
txt: ./txt/cord-266564-imj1lcy9.txt
cache: ./cache/cord-266564-imj1lcy9.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.02.028
doi: 10.1016/j.jinf.2020.02.028
abstract: nan
summary:
  Given the maternal physiologic and immune function changes in pregnancy [2] , pregnant individuals might face greater risk of getting infected by SARS-CoV-2 and might have more complicated clinical events. We described epidemiological, clinical characteristics, pregnancy and perinatal outcomes of all hospitalized pregnant patients diagnosed with COVID-19 in China. We identified all hospitalized pregnant patients with laboratory-confirmed SARS-CoV-2 infection between December 8, 2019, and February 25, 2020 officially reported by the central government, in areas outside Wuhan, China. We reported 13 pregnant COVID-19 patients in China, indicating pregnant women also susceptible to SARS-CoV-2. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China


id: cord-267621-oc8bw7ft
author: Kevorkian, Jean-Philippe
date: 2020-09-01
txt: ./txt/cord-267621-oc8bw7ft.txt
cache: ./cache/cord-267621-oc8bw7ft.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32888976/
doi: 10.1016/j.jinf.2020.08.045
abstract: nan
summary:
  title: Early short-course corticosteroids and furosemide combination to treat non-critically ill COVID-19 patients: An observational cohort study 5 Therefore, to address the effectiveness of early short-course corticosteroid/furosemide treatment in the non-critically ill COVID-19 patient, we designed a retrospective observational cohort study. In the corticosteroid/furosemide treatment group, incidence of invasive MV or death given once daily for up to ten days reduced 28-day mortality by one-third among mechanically ventilated COVID-19 patients and by one-fifth among patients treated with oxygen, while no benefit was observed in patients not receiving respiratory support at randomization. To conclude, our data provides evidence that early short-course of corticosteroids combined to furosemide reduces the risk of invasive MV requirement or 28-day mortality in the non-critically ill COVID-19 patients.

title:
  Early short-course corticosteroids and furosemide combination to treat non-critically ill COVID-19 patients: An observational cohort study


id: cord-269389-x8i5x62v
title: The concept of quarantine in history: from plague to SARS
author: Gensini, Gian Franco
date: 2004-04-12
txt: ./txt/cord-269389-x8i5x62v.txt
cache: ./cache/cord-269389-x8i5x62v.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15474622/
doi: 10.1016/j.jinf.2004.03.002
summary:
  Measures analogous to those employed against the plague have been adopted to fight against the disease termed the Great White Plague, i.e. tuberculosis, and in recent times various countries have set up official entities for the identification and control of infections. The concept of (modern) preventive quarantine is strictly related to plague and dates back to 1377, when the Rector of the seaport of Ragusa, today called Dubrovnik (Croatia), officially issued the socalled ''trentina'' (an Italian word derived from ''trenta'', that is, the number 30), a 30-day isolation period. 10 More recently (2003) the proposal of the constitution of a new European monitoring, regulatory and research institution was made, since the already available system of surveillance, set up in Europe to control the onset of epidemics, came up against an enormous challenge in the global emergency of the severe acute respiratory syndrome (SARS).

abstract:
  The concept of ‘quarantine’ is embedded in health practices, attracting heightened interest during episodes of epidemics. The term is strictly related to plague and dates back to 1377, when the Rector of the seaport of Ragusa (then belonging to the Venetian Republic) officially issued a 30-day isolation period for ships, that became 40 days for land travellers. During the next 100 years similar laws were introduced in Italian and in French ports, and they gradually acquired other connotations with respect to their original implementation. Measures analogous to those employed against the plague have been adopted to fight against the disease termed the Great White Plague, i.e. tuberculosis, and in recent times various countries have set up official entities for the identification and control of infections. Even more recently (2003) the proposal of the constitution of a new European monitoring, regulatory and research institution has been made, since the already available system of surveillance has found an enormous challenge in the global emergency of the severe acute respiratory syndrome (SARS). In the absence of a targeted vaccine, general preventive interventions have to be relied upon, including high healthcare surveillance and public information. Quarantine has, therefore, had a rebound of celebrity and updated evidence strongly suggests that its basic concept is still fully valid.


id: cord-270258-9vgpphiu
author: Ko, Jae-Hoon
date: 2016-08-09
txt: ./txt/cord-270258-9vgpphiu.txt
cache: ./cache/cord-270258-9vgpphiu.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445316302092
doi: 10.1016/j.jinf.2016.08.005
summary:
  To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we evaluated MERS-CoV infected patients managed in a tertiary care center during the 2015 MERS outbreak in Korea. To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we reviewed the electronic medical records of who were diagnosed with MERS-CoV infection and admitted at Samsung Medical Center, a 1950 tertiary care university hospital which managed the largest number of MERS-CoV infected patients as a single center during the 2015 Korean MERS outbreak. The present analysis of predictive factors for pneumonia development and progression to respiratory failure using variables obtained by day 3 of symptom onset could be conducted owing to the observation of entire clinical course of the disease from the exposure to MERS-CoV.

title:
  Predictive factors for pneumonia development and progression to respiratory failure in MERS-CoV infected patients

abstract:
  BACKGROUND: After the 2015 Middle East respiratory syndrome (MERS) outbreak in Korea, prediction of pneumonia development and progression to respiratory failure was emphasized in control of MERS outbreak. METHODS: MERS-CoV infected patients who were managed in a tertiary care center during the 2015 Korean MERS outbreak were reviewed. To analyze predictive factors for pneumonia development and progression to respiratory failure, we evaluated clinical variables measured within three days from symptom onset. RESULTS: A total of 45 patients were included in the study: 13 patients (28.9%) did not develop pneumonia, 19 developed pneumonia without respiratory failure (42.2%), and 13 progressed to respiratory failures (28.9%). The identified predictive factors for pneumonia development included age ≥45 years, fever ≥37.5 °C, thrombocytopenia, lymphopenia, CRP ≥ 2 mg/dL, and a threshold cycle value of PCR less than 28.5. For respiratory failure, the indicators included male, hypertension, low albumin concentration, thrombocytopenia, lymphopenia, and CRP ≥ 4 mg/dL (all P < 0.05). With ≥ two predictive factors for pneumonia development, 100% of patients developed pneumonia. Patients lacking the predictive factors did not progress to respiratory failure. CONCLUSION: For successful control of MERS outbreak, MERS-CoV infected patients with ≥ two predictive factors should be intensively managed from the initial presentation.


id: cord-271957-osaycpe8
author: Zuin, Marco
date: 2020-04-11
txt: ./txt/cord-271957-osaycpe8.txt
cache: ./cache/cord-271957-osaycpe8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32283158/
doi: 10.1016/j.jinf.2020.03.059
abstract: nan
summary:
  title: Arterial hypertension and risk of death in patients with COVID-19 infection: systematic review and meta-analysis Also other recent investigations have reported a higher prevalence of cardiovascular disease (CVD) and a direct association between the severity of COVID-19 infection [2] . However, to the best of our knowledge, no previous meta-analyses have globally estimated the risk of death in hypertensive patients with COVID-19 infection. We therefore perform a systematic review and meta-analysis to evaluate the risk of death in COVID-19 infection patients with and without HT. The analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement (Supplementary file 1) [3] . Our brief meta-analysis demonstrated that patients with COVID-19 infection and HT have a significant high mortality risk. Prevalence of comorbidities in the novel Wuhan coronavirus (COVID-19) infection: a systematic review and metaanalysis

title:
  Arterial hypertension and risk of death in patients with COVID-19 infection: systematic review and meta-analysis


id: cord-273751-61eeykj1
author: Yang, Zhenwei
date: 2020-04-10
txt: ./txt/cord-273751-61eeykj1.txt
cache: ./cache/cord-273751-61eeykj1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.03.062
doi: 10.1016/j.jinf.2020.03.062
summary:
  title: The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis The inclusion criteria in this meta-analysis were as follows: (1) subjects in each study were patients with coronavirus infection; (2) the patients were divided into the experimental group using corticosteroids and the control group not using corticosteroids; (3) the outcomes included the use of corticosteroids in critical and noncritical patients, mortality, length of stay (LOS) and adverse reactions to corticosteroids. We extracted the following variables: the authors, the publication year, the study design, viral type, population, treatment details (including corticosteroid use, types and doses of corticosteroids, and other treatments), and outcome measures such as the use of corticosteroids in critical and non-critical patients, mortality, LOS and adverse reactions to corticosteroids (including bacterial infection, hyperglycemia, hypocalcemia and hypokalemia). In this systematic review and meta-analysis, the result indicated that patients with severe conditions were more likely to require corticosteroids therapy.

title:
  The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis

abstract:
  OBJECTIVES: An outbreak of novel coronavirus in 2019 threatens the health of people, and there is no proven pharmacological treatment. Although corticosteroids were widely used during outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, their efficacy remainedhighly controversial. We aimed to further evaluate the influence of corticosteroids on patients with coronavirus infection. METHODS: We conducted a comprehensive search of literature published in PubMed, Embase, Cochrane library, and China National Knowledge Infrastructure (CNKI) from January 1, 2002 to March 15, 2020. All statistical analyses in this study were performed on stata14.0. RESULTS: A total of 5270 patients from 15 studies were included in this meta-analysis. The result indicated that critical patients were more likely to require corticosteroids therapy (risk ratio [RR] = 1.56, 95% confidence interval [CI] = 1.28-1.90, P<0.001). However, corticosteroid treatment was associated with higher mortality (RR = 2.11, 95%CI = 1.13-3.94, P = 0.019), longer length of stay (weighted mean difference [WMD] = 6.31, 95%CI = 5.26–7.37, P<0.001), a higher rate of bacterial infection (RR = 2.08, 95%CI = 1.54–2.81, P<0.001), and hypokalemia (RR = 2.21, 95%CI = 1.07–4.55, P = 0.032) but not hyperglycemia (RR = 1.37, 95%CI=0.68–2.76, P = 0.376) or hypocalcemia (RR = 1.35, 95%CI = 0.77–2.37, P = 0.302). CONCLUSIONS: Patients with severe conditions are more likely to require corticosteroids. Corticosteroid use is associated with increased mortality in patients with coronavirus pneumonia.


id: cord-276328-08ava9ni
title: Hepatic manifestations and complications of COVID-19: A systematic review and meta-analysis
author: Kunutsor, Setor K.
date: 2020-06-21
txt: ./txt/cord-276328-08ava9ni.txt
cache: ./cache/cord-276328-08ava9ni.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32579984/
doi: 10.1016/j.jinf.2020.06.043
abstract: nan
summary:
  title: Hepatic manifestations and complications of COVID-19: A systematic review and meta-analysis (1, 2) In addition to the observation that older patients, males and those with pre-existing comorbidities such as cardiovascular disease, diabetes, chronic kidney disease and chronic liver disease are at highest risk for severe illness or death, (3, 4) COVID-19 complications have been shown to correlate with the disease severity or mortality. Renal complications in COVID-19: A systematic review and meta-analysis Cardiovascular complications in COVID-19: A systematic review and meta-analysis Markers of liver injury and clinical outcomes in COVID-19 patients: A systematic review and meta-analysis Cardiovascular Implications of Fatal Outcomes of Patients With Coronavirus Disease 2019 (COVID-19) Comorbid Chronic Diseases and Acute Organ Injuries Are Strongly Correlated with Disease Severity and Mortality among COVID-19 Patients: A Systemic Review and Meta-Analysis. Longitudinal association between markers of liver injury and mortality in COVID-19 in China


id: cord-276991-gv1k7u7j
title: Strategies to trace back the origin of COVID-19
author: Zhang, Xu
date: 2020-04-08
txt: ./txt/cord-276991-gv1k7u7j.txt
cache: ./cache/cord-276991-gv1k7u7j.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.03.032
doi: 10.1016/j.jinf.2020.03.032
abstract: nan
summary:
  The recent outbreak of coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2, had raised great concern. Chinese authorities originally announced that the first infection case was reported on December 31, 2019, and many of the initial cases were linked directly to Huanan seafood market in Wuhan, in the Hubei province. The hypothesis that the outbreak originated at the market, with its initial transmission from live animals to human beings followed by rapid human-to-human transmission, is suggested to be most likely and convincing. Emergence of SARS-like coronavirus poses new challenge in China Novel coronavirus disease (Covid-19): the first two patients in the UK with person to person transmission Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Emergence of SARS-like coronavirus in china: an update


id: cord-277705-6lgt2i7f
title: A potential inhibitory role for integrin in the receptor targeting of SARS-CoV-2
author: Luan, Junwen
date: 2020-04-10
txt: ./txt/cord-277705-6lgt2i7f.txt
cache: ./cache/cord-277705-6lgt2i7f.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S016344532030181X?v=s5
doi: 10.1016/j.jinf.2020.03.046
abstract: nan
summary:
  An RGD motif (403-405) was identified in SARS-CoV-2 S protein ( Figure 1A ). These results suggested that RGD/KGD integrin-binding motif is conserved in several coronaviruses including SARS-CoV-2 and SARS-CoV. To investigate whether RGD/KGD motif in S proteins from SARS-CoV-2 We identified a KGD motif in 353-355 of ACE2 (BAB40370.1), which is a key region for binding S protein ( Figure 1F ). Integrin associates with ACE2 through its KGD motif including K353, which is one of key AAs for S protein recognition. Integrin associates with S protein by its RGD/KGD motif, which would shield the space of RBM for contacting with ACE2. Because RGD recognized a broader spectrum of integrins than KGD, more integrins could block receptor binding of SARS-CoV-2 S than that of SARS-CoV S. In conclusion, we identified an RGD/KGD integrin-binding motif in S proteins from SARS-CoV-2 and SARS-CoV.


id: cord-277763-ihg3te63
title: The role of healthcare staff COVID-19 screening in infection prevention & control
author: Moynan, David
date: 2020-06-25
txt: ./txt/cord-277763-ihg3te63.txt
cache: ./cache/cord-277763-ihg3te63.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320304382
doi: 10.1016/j.jinf.2020.06.057
abstract: nan
summary:
  While HCW can acquire infections and contribute to cross-transmission during hospital outbreaks such as influenza or norovirus, asymptomatic staff are usually not routinely screened as part of the outbreak control measures. In March and April 2020, on three wards with two or more positive COVID-19 patients after three days of admission (designated as potential nosocomial infection), we implemented universal staff SARS-CoV-2 testing on that ward as part of outbreak management. As asymptomatic (or indeed, pre-symptomatic) HCW may have similar viral loads and may be capable of transmission as much as symptomatic individuals 9 , their detection and subsequent exclusion from work is an important aspect of a hospital''s COVID-19 strategy. In conclusion, as hospitals begin to reopen to routine non-COVID-19 services, HCW SARS-CoV-2 testing irrespective of symptoms should be considered, particularly as part of outbreak management to rapidly prevent onward transmission to patients and other staff. COVID-19: PCR Screening of Asymptomatic Health-Care Workers at London Hospital


id: cord-278225-d0gxb6bx
author: Meng, Yifan
date: 2020-04-30
txt: ./txt/cord-278225-d0gxb6bx.txt
cache: ./cache/cord-278225-d0gxb6bx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.04.036
doi: 10.1016/j.jinf.2020.04.036
abstract: nan
summary:
  title: Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients It has been emphasized that diagnostic testing for SARS-CoV-2 was an especially important tool in the diagnosis and management of patients with COVID-19. All patients included in the present study were verified as positive for SARS-CoV-2 infection by reverse transcriptase polymerase chain reaction (RT-PCR). At present clinical practice, patients with improved respiratory symptoms, improved pulmonary imaging, and nucleic acid tests negative twice consecutively (sampling interval ≥ 24 hours) can be discharged. reported that potential false-negative nucleic acid testing results for SARS-CoV-2 could be caused by thermal inactivation of samples with low viral loads. Value of Diagnostic Testing for SARS-CoV-2/COVID-19 Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19 Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads

title:
  Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients


id: cord-280188-gir0y1m1
author: Wang, Yanqun
date: 2016-06-13
txt: ./txt/cord-280188-gir0y1m1.txt
cache: ./cache/cord-280188-gir0y1m1.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445316301232
doi: 10.1016/j.jinf.2016.05.014
summary:
  title: Genetic characterization of human bocavirus among children with severe acute respiratory infection in China OBJECTIVES: To investigate the genetic character of Human bocavirus (HBoV) among children with severe acute respiratory infection (SARI) in China. The nucleotide deletions and substitutions occurred in NP1 and VP1 represented novel molecular signatures enabling subtype differentiation between HBoVs. CONCLUSIONS: We described some new characteristics in the epidemiology of HBoV among children with SARI, these data will significantly expand the current knowledge of HBoV epidemic and genomic characterization among children with SARI. Through high-throughput sequencing, four complete genomes of HBoV were obtained (KM464728, KM464729, Figure 1 Phylogenetic analysis of HBoV detected among Children with SARI. However, the infection rates of HBoV among hospitalized children with SARI in three different regions were almost consistent (21.6%, 22.5% and 17.7%). Surveillance and genome analysis of human bocavirus in patients with respiratory infection in

title:
  Genetic characterization of human bocavirus among children with severe acute respiratory infection in China

abstract:
  OBJECTIVES: To investigate the genetic character of Human bocavirus (HBoV) among children with severe acute respiratory infection (SARI) in China. METHODS: We screened 993 respiratory samples for HBoV by PCR among hospitalized children with SARI between September 2007 and March 2014. Four of HBoV1 samples were selected for complete genomes analysis by next-generation sequencing. RESULTS: The results show that 200 (20.1%) out of 993 samples were HBoV-positive, most of these HBoV belong to HBoV1 subtype (n = 197), HBoV2 (n = 1) and HBoV3 (n = 2) were also detected. Fifty (5.04%) of 993 SARI patient were detected as HBoV-positive only. Four HBoV1 genomes in this study were conserved and showed no significant difference among the nucleotide diversity from different regions. Analyses of evolutionary rates showed that NS1 exhibited the highest degree of conservation while the VP1 gene exhibited the fastest rate of evolution at 4.20 × 10(−4) substitutions/site/year. The nucleotide deletions and substitutions occurred in NP1 and VP1 represented novel molecular signatures enabling subtype differentiation between HBoVs. CONCLUSIONS: We described some new characteristics in the epidemiology of HBoV among children with SARI, these data will significantly expand the current knowledge of HBoV epidemic and genomic characterization among children with SARI.


id: cord-280350-ay4cnzn5
title: Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus
author: Chan, Jasper F.W.
date: 2013-10-03
txt: ./txt/cord-280350-ay4cnzn5.txt
cache: ./cache/cord-280350-ay4cnzn5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24096239/
doi: 10.1016/j.jinf.2013.09.029
summary:
  We then assessed the anti-MERS-CoV activities of the identified compounds and of interferons, nelfinavir, and lopinavir because of their reported anti-coronavirus activities in terms of cytopathic effect inhibition, viral yield reduction, and plaque reduction assays in Biosafety Level-3 laboratory. Given the limited time available to develop novel anti-MERS-CoV agents in this evolving epidemic, we attempted to provide an alternative solution by identifying potential broad-spectrum antiviral agents against MERS-CoV and influenza A viruses by a small compound-based forward chemical genetics approach using chemical libraries consisting of 1280 drug compounds already marketed or having reached clinical trials in the United States, Europe, or Asia (Microsource Discovery Systems, USA). 25 We then assessed the anti-MERS-CoV activities of the identified drug compounds in cell culture by cytopathic effect (CPE) inhibition, viral yield reduction, and plaque reduction assay (PRA) assays, as well as drug cytotoxicity.

abstract:
  OBJECTIVES: Middle East respiratory syndrome coronavirus (MERS-CoV) has emerged to cause fatal infections in patients in the Middle East and traveler-associated secondary cases in Europe and Africa. Person-to-person transmission is evident in outbreaks involving household and hospital contacts. Effective antivirals are urgently needed. METHODS: We used small compound-based forward chemical genetics to screen a chemical library of 1280 known drugs against influenza A virus in Biosafety Level-2 laboratory. We then assessed the anti-MERS-CoV activities of the identified compounds and of interferons, nelfinavir, and lopinavir because of their reported anti-coronavirus activities in terms of cytopathic effect inhibition, viral yield reduction, and plaque reduction assays in Biosafety Level-3 laboratory. RESULTS: Ten compounds were identified as primary hits in high-throughput screening. Only mycophenolic acid exhibited low EC(50) and high selectivity index. Additionally, ribavirin and interferons also exhibited in-vitro anti-MERS-CoV activity. The serum concentrations achievable at therapeutic doses of mycophenolic acid and interferon-β1b were 60–300 and 3–4 times higher than the concentrations at which in-vitro anti-MERS-CoV activities were demonstrated, whereas that of ribavirin was ∼2 times lower. Combination of mycophenolic acid and interferon-β1b lowered the EC(50) of each drug by 1–3 times. CONCLUSIONS: Interferon-β1b with mycophenolic acid should be considered in treatment trials of MERS.


id: cord-280544-1rhu478r
author: Korte, Wolfgang
date: 2020-08-25
txt: ./txt/cord-280544-1rhu478r.txt
cache: ./cache/cord-280544-1rhu478r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32853597/
doi: 10.1016/j.jinf.2020.08.032
abstract: nan
summary:
  title: SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on antibodies rapidly decline early on 1, 3 Wolfgang Korte*, 2,3 Marija Buljan, 2,3 Matthias Rösslein, 2,3 Peter Wick, 1 Valentina Golubov, 1 Jana Jentsch, 1 Michael Reut, 3, 4 Karen Peier, 3 Brigitte Nohynek, 3 Aldo Fischer, 3 Raphael Stolz, 3 This cohort study included patients with a history of a positive SARS-CoV-2 PCR test. Results of the antibody course in 159 participants (52·2% females, 47·8% males), effectively spanning the time frame of two to ten weeks after a positive SARS-CoV-2 PCR test, are provided. The decline is statistically significant for anti-SP and anti-NC IgG at weeks 8-10 ( Figure 1) ; this is remarkable, as a continued IgG response for more than 34 weeks was seen with the SARS-CoV(-1) outbreak 6 . Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

title:
  SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on


id: cord-280829-juu8d60q
author: Anathallee, Mohammad
date: 2006-06-09
url: https://www.sciencedirect.com/science/article/pii/S0163445306001393
doi: 10.1016/j.jinf.2006.03.034
title:
  Emergency departments (EDs) in the United Kingdom (UK) are not prepared for emerging biological threats and bioterrorism

abstract:
  OBJECTIVE: To assess the preparedness of emergency departments (EDs) in the United Kingdom (UK) for the management of potential biological incidents. METHODS: We telephoned all hospitals in the UK listed as having a major ED. We surveyed their ED facilities and procedures for managing patients with infectious diseases. We determined how many of the EDs had an isolation room available and, if present, whether this had an independent ventilation system and separate access from outside the ED. In addition, we determined how many of the EDs would isolate patients with suspected cases of chickenpox, tuberculosis (TB), severe acute respiratory syndrome (SARS) and other suspicious infections. RESULTS: We obtained complete data from 203 (79%) of the 257 hospitals approached. Only 49 (24%) of these hospitals had isolation facilities available in the ED. Of these 49 EDs, 30 (61%) reported an independent ventilation system and 18 (37%) reported a separate access from outside the ED. The majority of EDs would isolate patients with potential infectious diseases, however, 47 (23%) would not isolate patients with suspected chickenpox, 37 (18%) EDS would not isolate patients with suspected TB, 12 (6%) EDS would not isolate patients with suspected SARS and 55 (27%) EDS would not isolate patients with other suspicious infections. CONCLUSION: EDs in the UK are not prepared for emerging biological threats and bioterrorism. With current facilities and procedures it is highly likely that an infectious agent will spread to staff and other patients in any future biological incident.


id: cord-281753-neur9nmc
author: Ji, Jingjing
date: 2020-11-08
txt: ./txt/cord-281753-neur9nmc.txt
cache: ./cache/cord-281753-neur9nmc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.11.001
doi: 10.1016/j.jinf.2020.11.001
abstract: nan
summary:
  title: Early, low-dose, short-term methylprednisolone decreased the mortality in critical COVID-19 patients: a multicenter retrospective cohort study Since critical patients were more likely to receive GC therapy, only severe type and critical type patients, according to clinical classification of the Chinese Recommendations for Diagnosis and Treatment of Novel Coronavirus (SARSCoV2) infection (Trial 7th version) 4 , were enrolled in present study. We retrospective collected the clinical and outcome data of critical COVID-19 patients, and taking methylprednisolone ( Few studies have discussed the application time, dosage and duration of MP, which were mostly based on the physician experience. To further clarify when and how to employ MP application on the critical type patients, the hazards ratios were analyzed in each group according to the starting time, dosage, and treatment duration ( Figure 2 ).

title:
  Early, low-dose, short-term methylprednisolone decreased the mortality in critical COVID-19 patients: a multicenter retrospective cohort study


id: cord-281984-en9825p9
author: Wang, Shijie
date: 2020-09-24
txt: ./txt/cord-281984-en9825p9.txt
cache: ./cache/cord-281984-en9825p9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32979408/
doi: 10.1016/j.jinf.2020.09.022
summary:
  title: Neutrophil-to-lymphocyte ratio at admission is an independent risk factors for the severity and mortality in patients with coronavirus disease 2019  The level of NLR at admission could be independent risk factors for the severe disease and the mortality of COVID-19.  The level of NLR at admission could be independent risk factors for the severe disease and the mortality of COVID-19. have been published in your journal and reported that the neutrophil-to-lymphocyte ratio (NLR) is an independent risk factor for the mortality of the COVID-19 patients. In conclusion, we found that the level of NLR at admission could be independent risk factors for the prognosis of COVID-19, not only for the mortality but also for the disease severity. Neutrophil-to-lymphocyte ratio as an independent risk factor for mortality in hospitalized patients with COVID-19

title:
  Neutrophil-to-lymphocyte ratio at admission is an independent risk factors for the severity and mortality in patients with coronavirus disease 2019

abstract:
  • The level of NLR at admission could be independent risk factors for the severe disease and the mortality of COVID-19. • The predictive value of NLR for poor prognosis was more significant in patients without other potential risk factors. • NLR could help physicians rapidly identify high-risk patients and adopt timely intervention.


id: cord-282053-ftjx29lw
author: Luis García de GuadianaRomualdo
date: 2020-08-12
txt: ./txt/cord-282053-ftjx29lw.txt
cache: ./cache/cord-282053-ftjx29lw.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320305430
doi: 10.1016/j.jinf.2020.08.010
abstract: nan
summary:
  We read the recent articles by Li and colleagues and Lin and colleagues about the role of two inflammatory biomarkers, serum amyloid A 1 and ferritin 2 , in the evaluation of severity in coronavirus disease 2019 (COVID-19) patients. Higher blood levels of inflammatory biomarkers in blood, such as C-reactive protein (CRP), ferritin and D-dimer, have been reported as predictors of a poor outcome in COVID-19 patients 5 . The role of biomarkers associated to inflammation other than those above mentioned, such as calprotectin or growth differentiation factor 15 (GDF-15), is less known. Recently, an experimental study showed a novel function of GDF-15 in the promotion of lung human rhinovirus and virus-associated inflammation, contributing to the severity of respiratory viral infection 10 . We have shown that circulating levels of two emerging inflammatory biomarkers, calprotectin and GDF-15, are significantly higher in COVID-19 patients who died, suggesting a potential role in the evaluation of prognosis in these patients.

title:
  Circulating levels of GDF-15 and calprotectin for prediction of in-hospital mortality in COVID-19 patients: a case series


id: cord-282433-p6jl9gxf
author: Tu, Xinyi
date: 2015-03-27
url: https://doi.org/10.1016/j.jinf.2015.03.006
doi: 10.1016/j.jinf.2015.03.006
title:
  Functional polymorphisms of the CCL2 and MBL genes cumulatively increase susceptibility to severe acute respiratory syndrome coronavirus infection

abstract:
  OBJECTIVES: To assess associations between the functional polymorphisms G-2518A at the chemokine (C–C motif) ligand 2 gene (CCL2) and mannose binding lectin (MBL) codon 54 variant (A/B) and susceptibility to SARS. METHODS: We genotyped the CCL2 G-2518A and MBL codon 54 variant (A/B) in 4 case–control populations of Chinese descent, totally consisting of 932 patients with SARS and 982 control subjects. RESULTS: Both the high-CCL2-producing GG genotype and the low-MBL-producing B allele were consistently associated with increased risks of SARS-CoV infection in all 4 case–control populations (joint P = 1.6 × 10(−4) and 4.9 × 10(−8), for CCL2 and MBL respectively), with no interaction between polymorphisms could be detected. Furthermore, all the 4 case–control studies demonstrated a cumulative effect on risk of SARS-CoV infection for the combination of polymorphisms (joint P = 1.3 × 10(−10)). However, tests using the area under the curve (AUC) indicated that at this stage, the polymorphisms were unlikely to be appropriate for risk prediction testing because of low AUC values (all <66%). Additionally, no association was observed between the polymorphisms and severity of SARS. CONCLUSIONS: The CCL2 G-2518A and MBL codon 54 variant have a significantly cumulative effect on increased risk of SARS-CoV infection.


id: cord-282499-baia5prj
title: The evolution of CT characteristics in the patients with COVID-19 pneumonia
author: Lei, Pinggui
date: 2020-03-19
txt: ./txt/cord-282499-baia5prj.txt
cache: ./cache/cord-282499-baia5prj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32201155/
doi: 10.1016/j.jinf.2020.03.014
abstract: nan
summary:
  Actually, the CT features are various at different stages in the patients with COVID-19 infection. Recently, the studies demonstrated that the CT findings were typical signs for diagnosis at different stages of COVID-19 pneumonia. 3 , 4 Particularly, ground glass opacities (GGO) and consolidation were the principal manifestation in the CT images (CT scans before onset of symptoms or CT scans done ≤ 1 week after symptom onset), and GGO was decreased with increasing the stages of COVID-19 pneumonia. 4 Therefore, knowing the corresponding CT feature of COVID-19 pneumonia at different stages, which could be helpful to precisely diagnose and understand CT characteristics of the novel coronavirus pneumonia beyond the radiological findings itself. Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2 Clinical characteristics and imaging manifestations of the 2019 novel coronavirus disease (COVID-19):a multi-center study in Wenzhou city Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study


id: cord-282821-qvtvpnrr
author: Thijsen, Steven
date: 2020-06-12
url: https://www.sciencedirect.com/science/article/pii/S0163445320303959?v=s5
doi: 10.1016/j.jinf.2020.06.015
abstract: nan
title:
  Elevated nucleoprotein-induced interferon-γ release in COVID-19 patients detected in a SARS-CoV-2 enzyme-linked immunosorbent spot assay


id: cord-283758-0z3jwwby
title: COVID-19: Outcomes of patients with confirmed COVID-19 re-admitted to hospital.
author: Rokadiya, S.
date: 2020-07-08
txt: ./txt/cord-283758-0z3jwwby.txt
cache: ./cache/cord-283758-0z3jwwby.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.07.007
doi: 10.1016/j.jinf.2020.07.007
abstract: nan
summary:
  We aimed to investigate clinical outcomes of patients with confirmed COVID-19 who were readmitted to hospital, in order to identify risk factors for patients discharged and subsequent management of COVID-19 in clinical practice. In the re-admission group, the average time before being re-admitted to hospital was 10 days (IQR 6 -15), with dyspnoea the presenting complaint in 13/25 (52%). As far as we are aware, this is the first study looking at clinical outcomes for patients with COVID-19 who were readmitted to hospital. However, the high mortality rate (24%), and the median and prevalence of low SpO2 results in patients re-admitted is concerning and warrants further studies to evaluate reasons for re-admission, ensuring appropriate safety-netting when discharged. Based on our data on the average time before re-presentation at 10 days, enhanced, personalised follow up at 7 days in a formalised COVID-19 clinic with radiological imaging and oxygen saturation recording using pulse oximetry probes may help early identification of those at risk of deterioration, thus preventing re-admission.


id: cord-284853-6efhdogi
author: Xie, Yun
date: 2020-04-10
txt: ./txt/cord-284853-6efhdogi.txt
cache: ./cache/cord-284853-6efhdogi.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320301729?v=s5
doi: 10.1016/j.jinf.2020.03.044
summary:
  Intravenous immunoglobulin(IVIG) has been clinically used as an adjunctive drug in the treatment of severe pneumonia caused by influenza [3] , but there is controversy about its therapeutic effect on COVID-19 pneumonia, despite inclusion in the seventh edition of the guidelines stating that it can be considered for use in severe and critically ill patients. For this reason, this study retrospectively observed the relationship between the prognosis of patients with severe and critical COVID-19 pneumonia and the adjuvant therapy of IVIG and explored whether IVIG could improve the clinical symptoms, laboratory examination and prognosis of these patients. In summary, initiation of IVIG as adjuvant treatment for COVID-19 pneumonia within 48 hours of admission to the ICU can reduce the use of mechanical ventilation, shorten the hospital length of stay, promote the early recovery of patients, and improve the effective treatment of patients to achieve significant clinical efficacy.

title:
  Effect of regular intravenous immunoglobulin therapy on prognosis of severe pneumonia in patients with COVID-19

abstract:
  • Initiation of IVIG as adjuvant treatment for COVID-19 pneumonia within 48 hours of admission to the ICU can reduce the use of mechanical ventilation . • Initiation of IVIG as adjuvant treatment for COVID-19 pneumonia within 48 hours of admission to the ICU can reduce hospital length of stay and length of stay in ICU. • Initiation of IVIG as adjuvant treatment for COVID-19 pneumonia within 48 hours of admission to the ICU can reduce 28-day mortality of patients with severe COVID-19 pneumonia.


id: cord-284862-nhihxog0
author: Kroemer, Marie
date: 2020-08-25
txt: ./txt/cord-284862-nhihxog0.txt
cache: ./cache/cord-284862-nhihxog0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32853599/
doi: 10.1016/j.jinf.2020.08.036
summary:
  Although the existence of SARS-CoV-2 specific T-cells has been described 2,3 , the frequency and the intensity of SARS-CoV-2 specific T-cell responses among mild illness and severe pneumonia convalescent COVID-19 patients remains to be investigated. In this prospective study, 60 patients who had COVID-19 were enrolled in a two cohorts study that were entitled mild illness (n=30) and severe pneumonia (n=30) at least 21 days after the first symptoms of ; Table 1 for CoV-N) might be explained by the sequence homology between structural proteins from various coronavirus suggesting the existence of cross reactive memory T-cells 5 . We observed that all patients with severe pneumonia had a positive serology index and most of them had at least one specific cellular response for SARS-CoV-2 proteins (28 out of 30). Specific T-cell responses for S, M and N proteins were simultaneously shown for 70.0% of severe pneumonia patients while only for 37.9% of mild illness patients (P=0.0191) (Fig. 1E) .

title:
  COVID-19 patients display distinct SARS-CoV-2 specific T-cell responses according to disease severity

abstract:
  Adaptive Immune responses generated by SARS-CoV-2 virus in convalescent patients according to disease severity remain poorly characterized. To this end, we designed a prospective study (NCT04365322) that included 60 COVID-19 convalescent patients (1-month post infection) in two cohorts respectively entitled mild illness and severe pneumonia. The monitoring of peripheral immune responses was performed using IFNᵧ ELISpot assay. The serology index of each patient was investigated at the same time. Patients with severe pneumonia were older and had more comorbidities than patients with mild illness. T-cell responses in term of frequency and intensity were clearly distinct between mild illness and severe pneumonia patients. Furthermore, our results demonstrated that recent history of COVID-19 did not hamper viral memory T-cell pool against common viruses (Cytomegalovirus, Epstein-Barr-virus and Flu-virus). The presence of potent adaptive immunity even in patients who underwent severe pneumonia sustain the rationale for the development of protective therapeutics against SARS-CoV-2.


id: cord-285179-26ey3fm8
author: Chan, Kwok-Hung
date: 2013-04-10
url: https://doi.org/10.1016/j.jinf.2013.03.015
doi: 10.1016/j.jinf.2013.03.015
title:
  Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests

abstract:
  OBJECTIVES: A severe acute respiratory syndrome (SARS)-like disease due to a novel betacoronavirus, human coronavirus EMC (HCoV-EMC), has emerged recently. HCoV-EMC is phylogenetically closely related to Tylonycteris-bat-coronavirus-HKU4 and Pipistrellus-bat-coronavirus-HKU5 in Hong Kong. We conducted a seroprevalence study on archived sera from 94 game-food animal handlers at a wild life market, 28 SARS patients, and 152 healthy blood donors in Southern China to assess the zoonotic potential and evidence for intrusion of HCoV-EMC and related viruses into humans. METHODS: Anti-HCoV-EMC and anti-SARS-CoV antibodies were detected using screening indirect immunofluorescence (IF) and confirmatory neutralizing antibody tests. RESULTS: Two (2.1%) animal handlers had IF antibody titer of ≥1:20 against both HCoV-EMC and SARS-CoV with neutralizing antibody titer of <1:10. No blood donor had antibody against either virus. Surprisingly, 17/28 (60.7%) of SARS patients had significant IF antibody titers with 7/28 (25%) having anti-HCoV-EMC neutralizing antibodies at low titers which significantly correlated with that of HCoV-OC43. Bioinformatics analysis demonstrated a significant B-cell epitope overlapping the heptad repeat-2 region of Spike protein. Virulence of SARS-CoV over other betacoronaviruses may boost cross-reactive neutralizing antibodies against other betacoronaviruses. CONCLUSIONS: Convalescent SARS sera may contain cross-reactive antibodies against other betacoronaviruses and confound seroprevalence study for HCoV-EMC.


id: cord-286014-cc99e24x
author: Jang, T.-N
date: 2003-11-05
txt: ./txt/cord-286014-cc99e24x.txt
cache: ./cache/cord-286014-cc99e24x.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445303001804
doi: 10.1016/j.jinf.2003.09.004
summary:
  To describe the clinical characteristics and outcomes of patients with severe acute respiratory syndrome (SARS). The first probable SARS patient in Taiwan returned from China via Hong Kong early in the global outbreak in February 2003. 7 We analyse the clinical, laboratory, and radiological features of patients with probable SARS who were seen at the Shin Kong Wu Ho-Su Memorial Hospital (SKMH) in Taipei, Taiwan. 16 In our study, SARS-associated coronavirus RNA was detected in oropharyngeal swabs by RT-PCR in 16 (55.1%) of 29 patients at initial presentation. Case definitions for surveillance of severe acute respiratory syndrome (SARS) A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome in Singapore: clinical features of index patient and initial contacts Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China

title:
  Severe acute respiratory syndrome in Taiwan: analysis of epidemiological characteristics in 29 cases

abstract:
  Objectives. To describe the clinical characteristics and outcomes of patients with severe acute respiratory syndrome (SARS). Methods. Between March 28 and June 30 '2003, 29 patients with probable SARS seen at Shin Kong Wu Ho-Su Memorial Hospital, Taipei, were analysed. Results. Presenting symptoms included fever (100%), cough (69.0%), chills or rigor (62.1%), and shortness of breath (41.4%). Mean days to defervescence were 6.8±2.9 days, but fever recurred in 15 patients (51.7%) at 10.9±3.4 days. Common laboratory features included lymphopenia (72.4%), thrombocytopenia (34.5%) and elevated C-reactive protein (CRP), lactate dehydrogenase (LDH), and aspartate aminotransferase (AST) (93.1, 62.1, 44.8%, respectively). All patients except one had initial abnormal chest radiographs and 20 (69.0%) had radiological worsening at 7.5±2.6 days. Nine patients (31.0%) subsequently required mechanical ventilation with four deaths (13.8%). Most patients with clinical deterioration responded to pulse corticosteroid therapy (14 out of 17) but six complicated with nosocomial infections. The risk factors associated with severe disease were presence of diarrhoea, high peak LDH and CRP, high AST and creatine kinase on admission and high peak values. Conclusions. Prudent corticosteroid use, vigilant microbiological surveillance and appropriate antibiotics coverage are the key to successful treatment.


id: cord-287030-xzothuf7
title: Emergency department evaluation of the febrile traveler
author: Pigott, David C.
date: 2006-05-23
txt: ./txt/cord-287030-xzothuf7.txt
cache: ./cache/cord-287030-xzothuf7.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445306001149
doi: 10.1016/j.jinf.2006.03.028
summary:
  While the presentation of a patient with undifferentiated febrile illness to the emergency department is rarely a cause for alarm, the additional factor of recent international travel suggests a host of unusual pathogens, some with the potential for rapid and devastating transmission among both patients and health care workers. 1,2 A prospective review of 195 febrile patients requiring admission after returning to the United Kingdom from the tropics found that while malaria (42%) was the most common cause for hospital admission, non-specific viral illness and bacterial infections (including urinary tract infection, community-acquired pneumonia and pharyngitis) accounted for 34% of patients. Expanding this methodology to account for other potential infectious agents that may present to a given hospital or emergency department can provide some guidance for clinicians who may encounter febrile patients who have recently returned from any geographic region, unwittingly harboring undiagnosed viral, bacterial or parasitic infection.

abstract:
  The emergency department evaluation of the febrile traveler presents the emergency physician with a set of unique and often challenging circumstances. In addition to evaluating and managing the usual array of community-acquired infections, the clinician must be prepared to diagnose and treat a host of uncommon and potentially life-threatening pathogens. This diseases range from widespread tropical diseases such as malaria to the more exotic and lethal viral hemorrhagic fevers. A thoughtful approach guided by geographic patterns of illness offers a reliable method for determining the most likely sources of fever in the returned traveler as well as a focused diagnostic and treatment strategy.


id: cord-287823-avi14ee5
title: The potential impact of vulnerability and coping capacity on the pandemic control of COVID-19
author: Wong, Martin CS
date: 2020-05-28
txt: ./txt/cord-287823-avi14ee5.txt
cache: ./cache/cord-287823-avi14ee5.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320303376
doi: 10.1016/j.jinf.2020.05.060
summary:
   We examined if these dimensions were associated with COVID-19 pandemic control  Higher vulnerability and poorer coping capacity were associated with poorer control  Modifying these two dimensions might potentially mitigate COVID-19 pandemic control Dear Editor, Worldwide, the coronavirus disease 2019 (COVID-19) has induced a substantial global burden. On the contrary, a recent study published in the Journal of Infection examined the association between country-specific global health security index (GHSI) and the burden of COVID-19, but the findings showed that countries with higher GHSI did not have higher COVID-19 rate and had greater number of COVID-19 cases and deaths. We aimed to evaluate if countries with lower vulnerability and higher coping capacity were associated with better control of the COVID-19 pandemic, as measured by incidence and mortality outcomes. From multivariate regression analysis ( Table 1) , countries with higher vulnerability were significantly associated with higher maximum 14-day cumulative incidence since the first case ( coefficient Our findings imply that reducing vulnerability and enhancing capacity to cope could potentially mitigate the COVID-19 pandemic.

abstract:
  • The European commission has developed an index for risk management named INFORM; • Two dimensions (vulnerability and lack of coping capacity) are relevant to COVID-19; • We examined if these dimensions were associated with COVID-19 pandemic control; • Higher vulnerability and poorer coping capacity were associated with poorer control; • Modifying these two dimensions might potentially mitigate COVID-19 pandemic control.


id: cord-288010-i9zrojoo
author: Jia, Yuanyuan
date: 2020-05-15
url: https://www.sciencedirect.com/science/article/pii/S0163445320302917?v=s5
doi: 10.1016/j.jinf.2020.05.016
abstract: nan
title:
  Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China


id: cord-288366-xe3pxrhv
author: Wellbelove, Zoe
date: 2020-10-25
txt: ./txt/cord-288366-xe3pxrhv.txt
cache: ./cache/cord-288366-xe3pxrhv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.10.015
doi: 10.1016/j.jinf.2020.10.015
abstract: nan
summary:
  title: Comparing the 4C mortality score for COVID-19 to established scores (CURB65, CRB65, qSOFA, NEWS) for respiratory infection patients Comparing the 4C mortality score for COVID-19 to established scores (CURB65, CRB65, qSOFA, NEWS) for respiratory infection patients We compared the newly validated 4C mortality score to the established CURB65, CRB65 and qSOFA scores in the prediction of 30-day mortality in a variety of existing respiratory infection cohorts in an exploratory analysis. Data from various previous studies performed in Dundee 3 , Hull 4 and South Yorkshire 5 of community-acquired pneumonia (CAP), invasive pneumococcal disease (IPD), and influenza (flu), respectively, plus a COVID-19 cohort (local ISARIC study patients 2 ) were analysed. The 4C mortality score had the greatest AUROC in COVID 19, CAP and IPD patients (0.83, 0.78 and 0.74, respectively) and had a similar AUROC, compared to the other scores (except NEWS, which was not calculable), in the influenza cohort (0.88).

title:
  Comparing the 4C mortality score for COVID-19 to established scores (CURB65, CRB65, qSOFA, NEWS) for respiratory infection patients


id: cord-288814-1zayb21f
title: Comorbidities for fatal outcome among the COVID-19 patients: a hospital-based case-control study
author: Lu, Qing-Bin
date: 2020-07-27
txt: ./txt/cord-288814-1zayb21f.txt
cache: ./cache/cord-288814-1zayb21f.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.07.026
doi: 10.1016/j.jinf.2020.07.026
abstract: nan
summary:
  Here by performing a retrospective multi-center study, we try to evaluate the adjusted effect of the common preexisting comorbidities on COVID-19 related death, based on which, the therapy effect of three widely used anti-hypertension drugs were assessed. By multivariate logistic regression model adjusting age, sex, and delay from symptom onset to hospital admission, six comorbidities showed significant association with the disease outcome, with malignancy exhibiting the highest risk of death, followed by CKD, CVD, hypertension, CHD, and DM ( Figure 1A and Table S2 ). DM was found to be a strong risk factor for adverse outcome, with its risky effect also observed in those aged 60~70 years, which was reported for the two earlier CoV infections, severe acute respiratory syndrome (7) and the Middle East respiratory syndrome (8) . We provided evidence 5 that CCB drugs offered beneficial effect of reducing risk for fatal outcome in hypertension-COVID-19 patients, mostly mediated through enhancing the recovery of abnormal parameters and reducing host inflammatory response that had been proven to aggravate the disease severity.


id: cord-289364-p31gt533
title: A case of SARS-CoV-2 re-infection
author: AlFehaidi, Alanoud
date: 2020-10-25
txt: ./txt/cord-289364-p31gt533.txt
cache: ./cache/cord-289364-p31gt533.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.10.019
doi: 10.1016/j.jinf.2020.10.019
abstract: nan
summary:
  Different reports have proposed the reactivation of SARS-CoV-2 infection, with 2 RT-PCR positive results following resolving symptoms and interim RT-PCR negative results [4] [5] [6] [7] [8] [9] [10] [11] . Early studies reported that re-detectable positive virus nucleic acid among patients with SARS-CoV-2 with an average duration of 15 days from discharge to a re-positive results 13 . Patients in those early reports did not show signs of infection with the second positive results and had negative swab results within one week later. The COCOREC (Collaborative study COvid RECurrences) study suggested that recurrence of infection is likely if the patient has two confirmed SARS-CoV-2 RT-PCR positive results over 15 days apart with one major clinical sign and no other cause to explain the symptoms. Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report


id: cord-290066-umthoftd
author: Jia, Xingwang
date: 2020-10-08
txt: ./txt/cord-290066-umthoftd.txt
cache: ./cache/cord-290066-umthoftd.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320306496
doi: 10.1016/j.jinf.2020.10.007
abstract: nan
summary:
  title: False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 We read with interest that antibody testing using a rapid immunochromatographic assay is reliable in the diagnosis of severe acute respiratory syndrome coronavirus 2 ( SARS-CoV-2 ) infection 1 . positive antibody results could be eliminated after five times dilution with normal human serum, when the RF level was lower than 10 IU/mL. The false positive antibody results could also be eliminated after 5 times dilution with normal human serum. Although the RT-PCR test has become the standard method for the diagnosis of SARS-CoV-2 infection, false-negative rates have been reported. Therefore, the combination of serum IgM/IgG antibody detection, the nucleic acid test, CT scan and clinical features improves the accuracy of COVID-19 diagnosis. Reliability and usefulness of a rapid IgM-IgG antibody test for the diagnosis of SARS-CoV-2 infection: A preliminary report

title:
  False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19


id: cord-290385-0smnl70i
title: Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease
author: Chan, Jasper F.W.
date: 2016-03-03
txt: ./txt/cord-290385-0smnl70i.txt
cache: ./cache/cord-290385-0smnl70i.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S016344531600061X
doi: 10.1016/j.jinf.2016.02.011
summary:
  Unlike its mosquito-borne relatives, such as dengue, West Nile, and Japanese encephalitis viruses, which can cause severe human diseases, Zika virus (ZIKV) has emerged from obscurity by its association with a suspected "congenital Zika syndrome", while causing asymptomatic or mild exanthematous febrile infections which are dengueor rubella-like in infected individuals. ZIKV RNA could be detected in breast milk and saliva of infected women, although replicative virus particles have not been demonstrated 78, 79 Perinatal transmission of other arboviruses, including DENV, CHIKV, WNV, and YFV, has also been reported. 115,120 74/ 8750 (0.8%) patients with suspected ZIKV infection in the French Polynesia outbreak developed neurological syndromes after presenting with a Zika fever-like illness. Zika fever-related death appears to be extremely rare but a number of probable cases have been reported, especially among immunocompromised patients and neonates with suspected congenital ZIKV infection.

abstract:
  Unlike its mosquito-borne relatives, such as dengue, West Nile, and Japanese encephalitis viruses, which can cause severe human diseases, Zika virus (ZIKV) has emerged from obscurity by its association with a suspected “congenital Zika syndrome”, while causing asymptomatic or mild exanthematous febrile infections which are dengue- or rubella-like in infected individuals. Despite having been discovered in Uganda for almost 60 years, <20 human cases were reported before 2007. The massive epidemics in the Pacific islands associated with the ZIKV Asian lineage in 2007 and 2013 were followed by explosive outbreaks in Latin America in 2015. Although increased mosquito breeding associated with the El Niño effect superimposed on global warming is suspected, genetic changes in its RNA virus genome may have led to better adaptation to mosquitoes, other animal reservoirs, and human. We reviewed the epidemiology, clinical manifestation, virology, pathogenesis, laboratory diagnosis, management, and prevention of this emerging infection. Laboratory diagnosis can be confounded by cross-reactivity with other circulating flaviviruses. Besides mosquito bite and transplacental transmission, the risk of other potential routes of transmission by transfusion, transplantation, sexual activity, breastfeeding, respiratory droplet, and animal bite is discussed. Epidemic control requires adequate clearance of mosquito breeding grounds, personal protection against mosquito bite, and hopefully a safe and effective vaccine.


id: cord-291181-u2t20mgi
title: Early signs that COVID-19 is being contained in Australia
author: Chin, Ken Lee
date: 2020-05-01
txt: ./txt/cord-291181-u2t20mgi.txt
cache: ./cache/cord-291181-u2t20mgi.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320302681
doi: 10.1016/j.jinf.2020.04.042
summary:
  4 In the present study, we report on the epidemiology of the COVID-19 outbreak in Australia observed thus far, as well as the predicted future numbers of cases, deaths and ICU admissions, and associated ICU costs. 5, 6 We forecasted the number of beds required for COVID-19 patients over time and its associated costs by applying the following conditions: (i) allocation of 10%, 30% and 50% of ICU beds for COVID-19; (ii) 3% (as currently observed in Australia), 5% (China) and 12% (Italy) of confirmed cases requiring intensive care 7 ; (iii) mean ICU stay between 7 and 14 days; and (iv) mean hospital stay prior to intensive care between 7 and 14 days. Based on extrapolation of trends prior to 29 March 2020, the Australian healthcare system would have been over-run by over 12,000 confirmed cases by 12 April 2020 (Supplement Figure C) .

abstract:
  • The COVID-19 pandemic is overwhelming many national healthcare networks. • Case fatality from COVID-19 infection in Australia is between 0.4% to 3.0%. • Strict public health measures were enforced to control this outbreak in Australia. • Australia is on its way joining China and South Korea in ‘flattening the curve’.


id: cord-291561-sxvgue36
author: Haixu, Liang
date: 2019-11-25
url: https://www.ncbi.nlm.nih.gov/pubmed/31778686/
doi: 10.1016/j.jinf.2019.11.014
abstract: nan
title:
  Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018


id: cord-291750-4s93wniq
title: Global COVID-19 fatality analysis reveals Hubei-like countries potentially with severe outbreaks
author: Lv, Boyan
date: 2020-04-14
url: https://www.ncbi.nlm.nih.gov/pubmed/32302605/
doi: 10.1016/j.jinf.2020.03.029
abstract:
  • CFR in Iran in the early stage of the outbreak is highest among all the countries. • CFRs in the USA and Italy are similar to Hubei Province in the early stage. • CFRs in South Korea are similar to outside Hubei, indicating less severity. • Our findings highlight the severity of outbreaks globally, particular in the USA.


id: cord-291960-1is0rv6c
author: Piñana, José Luis
date: 2019-02-21
url: https://api.elsevier.com/content/article/pii/S0163445319300581
doi: 10.1016/j.jinf.2019.02.009
title:
  Pulmonary cytomegalovirus (CMV) DNA shedding in allogeneic hematopoietic stem cell transplant recipients: Implications for the diagnosis of CMV pneumonia

abstract:
  OBJECTIVES: To date no definitive cut-off value for cytomegalovirus (CMV) DNA load in bronchoalveolar lavage (BAL) fluid specimens has been established to discriminate between CMV pneumonia and pulmonary CMV DNA shedding in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients. METHODS: The current retrospective study is aimed at assessing the range of CMV DNA loads quantified in BAL fluid specimens from allo-HSCT patients with pneumonia in which different microorganisms were causally involved. RESULTS: A total of 144 BAL specimens from 123 patients were included. CMV DNA was detected in 56 out of 144 BAL fluid specimens and the median CMV DNA load from patients in whom CMV pneumonia was unlikely or could be tentatively ruled out was 1210 (31–68, 920) IU/ml. The frequency of CMV DNA detection and median CMV DNA loads were comparable, irrespective of the attributable cause of pneumonia. Detection of CMV DNA loads in BAL fluid specimens >500 IU/ml was independently associated with pneumonia-attributable mortality. CONCLUSIONS: The current study highlights the difficulty in establishing universal CMV DNA load thresholds in BAL fluid specimens for distinguishing between CMV pneumonia and pulmonary CMV DNA shedding, and suggests that the presence of CMV DNA in BAL fluid specimens beyond a certain level may have a deleterious impact on patient outcome.


id: cord-292201-e7k7gn9q
title: Mass masking as a way to contain COVID-19 and exit lockdown in low- and middle-income countries
author: Fodjo, Joseph Nelson Siewe
date: 2020-07-17
url: https://doi.org/10.1016/j.jinf.2020.07.015
doi: 10.1016/j.jinf.2020.07.015
abstract:
  In new guidelines published on June 5(th) 2020, the World Health Organization (WHO) recommends that in areas with ongoing COVID-19 community transmission, governments should encourage the general public to wear face masks in specific situations and settings as part of a comprehensive approach to suppress COVID-19 transmission. Recent online surveys in 206,729 persons residing in nine low- and middle-income countries showed that 32.7%-99.7% of respondents used face masks with significantly differences across age groups and sexes. Targeted health promotion strategies and government support are required to increase mask use by the general population.


id: cord-293714-s6ezxi5r
title: The role of infection in Kawasaki syndrome
author: Principi, Nicola
date: 2013-04-18
url: https://www.sciencedirect.com/science/article/pii/S0163445313000777
doi: 10.1016/j.jinf.2013.04.004
abstract:
  OBJECTIVES: To analyse the evidence suggesting a possible infectious origin of Kawasaki syndrome (KS). METHODS: PubMed was searched for all of the studies published over the last 15 years using the key words “Kawasaki syndrome” or “mucocutaneous lymph node syndrome” and “infectious disease” or “genetics” or “vasculitis” or “pathogenesis”. RESULTS: Various levels of evidence support the hypothesis that KS is a complex disease triggered by an infection due to one or more pathogens. Viruses or bacteria may be the primum movens, although no specific infectious agent can be considered definitely etiological. A number of genetic polymorphisms have been identified in subjects with KS, but none of them can currently be considered a real marker of susceptibility. CONCLUSIONS: Various data suggest that KS is intimately related to infectious diseases and that its clinical expression is influenced by predisposing genetic backgrounds, but our knowledge of the infectious agent(s) involved and the genetic characteristics of susceptible children remains only partial. Further studies are needed to address the many still open questions concerning the disease.


id: cord-295074-fsbp4fky
author: Broor, Shobha
date: 2013-11-21
url: https://doi.org/10.1016/j.jinf.2013.11.005
doi: 10.1016/j.jinf.2013.11.005
title:
  Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India

abstract:
  OBJECTIVES: Though respiratory viruses are thought to cause substantial morbidity globally in children aged <5 years, the incidence of severe respiratory virus infections in children is unknown in India where 20% of the world's children live. METHODS: During August 2009–July 2011, prospective population-based surveillance was conducted for hospitalizations of children aged <5 years in a rural community in Haryana State. Clinical data and respiratory specimens were collected. Swabs were tested by RT-PCR for influenza and parainfluenza viruses, respiratory syncytial virus (RSV), human metapneumovirus, coronaviruses, and adenovirus. Average annual hospitalization incidence was calculated using census data and adjusted for hospitalizations reported to occur at non-study hospitals according to a comunity healthcare utilization survey. RESULTS: Of 245 hospitalized children, respiratory viruses were detected among 98 (40%), of whom 92 (94%) had fever or respiratory symptoms. RSV accounted for the highest virus-associated hospitalization incidence (34.6/10,000, 95% CI 26.3–44.7) and 20% of hospitalizations. There were 11.8/10,000 (95% CI 7.9–18.4) influenza-associated hospitalizations (7% of hospitalizations). RSV and influenza virus detection peaked in winter (November–February) and rainy seasons (July), respectively. CONCLUSION: Respiratory viruses were associated with a substantial proportion of hospitalizations among young children in a rural Indian community. Public health research and prevention in India should consider targeting RSV and influenza in young children.


id: cord-298639-v9yg80jw
title: High SARS-CoV-2 Antibody Prevalence among Healthcare Workers Exposed to COVID-19 Patients
author: Chen, Yuxin
date: 2020-06-04
txt: ./txt/cord-298639-v9yg80jw.txt
cache: ./cache/cord-298639-v9yg80jw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32504745/
doi: 10.1016/j.jinf.2020.05.067
summary:
  Risk analysis revealed that wearing face mask could reduce the infection risk (odds ratio [OR], 0.127, 95% confidence interval [CI] 0.017, 0.968), while when exposed to COVID-19 patients, doctors might have higher risk of seroconversion (OR, 346.837, 95% CI 8.924, 13479.434), compared with HCWs exposed to colleagues as well as nurses and general service assistants who exposed to patients. Our study revealed that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. Briefly, 96-well plates were coated with 500 ng/mL of recombinant RBD or NP protein overnight, incubating with diluted were also collected and the nasopharyngeal swab samples from these patients have been repeatedly tested as negative for SARS-CoV-2 RNA at least twice at a two-day apart. Our study proved that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients.

abstract:
  The seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was examined among 105 healthcare workers (HCWs) exposed to four patients who were laboratory confirmed with coronavirus disease 2019 (COVID-19), the disease caused by SARS-CoV-2 infection. These HCWs were immediately under quarantine for 14 days as soon as they were identified as close contacts. The nasopharyngeal swab samples were collected on the first and 14(th) day of the quarantine, while the serum samples were obtained on the 14(th) day of the quarantine. With the assay of enzyme immunoassay (EIA) and microneutralization assay, 17.14% (18/105) of HCWs were seropositive, while their swab samples were found to be SARS-CoV-2 RNA negative. Risk analysis revealed that wearing face mask could reduce the infection risk (odds ratio [OR], 0.127, 95% confidence interval [CI] 0.017, 0.968), while when exposed to COVID-19 patients, doctors might have higher risk of seroconversion (OR, 346.837, 95% CI 8.924, 13479.434), compared with HCWs exposed to colleagues as well as nurses and general service assistants who exposed to patients. Our study revealed that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients.


id: cord-299018-eo73yl4v
author: Gandini, O.
date: 2020-09-15
txt: ./txt/cord-299018-eo73yl4v.txt
cache: ./cache/cord-299018-eo73yl4v.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.09.006
doi: 10.1016/j.jinf.2020.09.006
abstract: nan
summary:
  title: Serum Ferritin as an independent risk factor for Acute Respiratory Distress Syndrome in COVID-19 Patients in Rome Italy Serum samples were collected from patients upon admission before starting any treatment and tested by Laboratory Department Of all patients included, 81 patients (57%) showed mild disease (control group) and 60 (43%) showed acute respiratory distress syndrome (ARDS) and systemic inflammation (severe group). 2 , panel C, D, E) Multivariate logistic regression model adjusted for several disease-related risk factors at admission, including age, sex, NLR, DD, LDH, ferritin and CRP, demonstrated that serum ferritin resulted as an independent predictor of disease severity in COVID-19 patients (OR = 1,0048, 95% CI, 1,0029 to 1,0083, P < 0,001.). We clearly demonstrated that serum levels of ferritin progressively increased with the severity of disease and correlate with poor prognosis in COVID-19 patients. Serum ferritin as an independent risk factor for severity in COVID-19 patients

title:
  Serum Ferritin as an independent risk factor for Acute Respiratory Distress Syndrome in COVID-19 Patients in Rome Italy


id: cord-300038-1fjb6b8e
title: Baricitinib therapy in COVID-19: A pilot study on safety and clinical impact
author: Cantini, Fabrizio
date: 2020-04-23
txt: ./txt/cord-300038-1fjb6b8e.txt
cache: ./cache/cord-300038-1fjb6b8e.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.04.017
doi: 10.1016/j.jinf.2020.04.017
summary:
  According to a recent report 3 , COVID-19, the disease caused by SARS-CoV-2, is characterized by three clinical patterns: no symptoms, mild to moderate disease, severe pneumonia requiring admission to Intensive Care Unit (ICU) in up to 31% of the patients 3 . On this basis, we assessed the safety of baricitinib therapy combined with lopinavir-ritonavir in moderate COVID-19 pneumonia patients and we evaluated its clinical impact. All consecutive hospitalized patients (March 16 th -30 th ) with moderate COVID-19 pneumonia, older than 18 years, were treated for 2 weeks with baricitinib tablets 4 mg/day added to ritonavirlopinavir therapy. The last consecutive patients with moderate COVID-19 pneumonia receiving standard of care therapy (lopinavir/ritonavir tablets 250 mg/bid and hydroxychloroquine 400 mg/day/orally for 2 weeks) admitted before the date of the first baricitinib-treated patient served as controls. These preliminary results on 12 patients with moderate COVID-19 pneumonia confirmed the safety of baricitinib therapy in a clinical context different from RA 7 .

abstract:
  • Baricitinib at 4 mg/day/orally was given to 12 patients with moderate COVID-19. • In baricitinib-treated patients no adverse events were recorded, after 2 weeks. • Clinical and respiratory parameters significantly improved at 2 weeks. • None of the baricitinib-treated patients required admission to ICU. • Proper control group was missing; this is required to demonstrate the efficacy.


id: cord-301491-frv4c5ny
author: Ran, Jinjun
date: 2020-07-08
url: https://api.elsevier.com/content/article/pii/S0163445320304655
doi: 10.1016/j.jinf.2020.07.011
title:
  The Ambient Ozone and COVID-19 Transmissibility in China: A Data-Driven Ecological Study of 154 Cities

abstract:
  • We quantified the COVID-19 transmissibility by the basic reproductive number. • The COVID-19 transmissibility could be negatively associated with ambient ozone. • The daily 1-h maximum ozone might cover 7.6% of the transmissibility variability. • It echoes a previous study of negative effects of ozone on the flu transmission. • The ground-level ozone may be a “double-edged sword” to public health.


id: cord-301592-n5ns3m34
author: Ivaska, Lauri
date: 2017-01-07
txt: ./txt/cord-301592-n5ns3m34.txt
cache: ./cache/cord-301592-n5ns3m34.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2017.01.002
doi: 10.1016/j.jinf.2017.01.002
summary:
  We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. 23e25 The aim of this study was to document the microbial causes of acute pharyngitis in children and adolescents in an outpatient setting and to evaluate the causative role of viruses by determining myxovirus resistance protein A (MxA) and other biomarker levels.

title:
  Aetiology of febrile pharyngitis in children: Potential of myxovirus resistance protein A (MxA) as a biomarker of viral infection

abstract:
  OBJECTIVES: Besides group A streptococcus (GAS), microbial causes of pharyngitis in children are not well known. We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. METHODS: In this prospective observational study, throat swabs and blood samples were collected from children (age 1–16 years) presenting to the emergency department with febrile pharyngitis. Microbial cause was sought by bacterial culture, polymerase chain reaction, and serology. Blood MxA level was determined. RESULTS: A potential pathogen was detected in 88% of 83 patients: GAS alone in 10%, GAS and viruses in 13%, group C or G streptococci alone in 2% and together with viruses in 3%, and viruses alone in 59% of cases. Enteroviruses, rhinoviruses, and adenoviruses were the most frequently detected viruses. Blood MxA levels were higher in children with viral (880 [245–1250] μg/L; median [IQR]) or concomitant GAS-viral (340 [150–710] μg/L) than in those with sole GAS (105 [80–160] μg/L) infections. CONCLUSIONS: Detection of respiratory viruses simultaneously with elevated blood MxA levels supports the causative role of viruses in the majority of children with pharyngitis.


id: cord-301744-rx7ywew5
title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality
author: Kelleni, Mina T.
date: 2020-08-15
txt: ./txt/cord-301744-rx7ywew5.txt
cache: ./cache/cord-301744-rx7ywew5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.08.018
doi: 10.1016/j.jinf.2020.08.018
abstract: nan
summary:
  title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality have reported SARS-CoV-2 viral load at diagnosis as an independent predictor of mortality. In a trial to explain the apparent contradictory results found in different studies as well as the lack of a distinct boundary between the viral loads that might be associated with a higher mortality rate or a higher recover rate; the author would like to suggest that SARS CoV-2 viral load should be only considered as a personalized reflection to the immune response to COVID-19 as well as to the genetic polymorphisms in SARS CoV-2 receptors 3 . ACE2 polymorphisms might be a better field of study than SARS CoV-2 viral load wishing to develop a genetic test that might predict and exempt, if possible, from COVID-19 related duty those who are more vulnerable to complications and mortality 4 SARS-CoV-2 viral load predicts COVID-19 mortality


id: cord-302855-wwg6x1df
author: Ma, Jia
date: 2020-04-14
txt: ./txt/cord-302855-wwg6x1df.txt
cache: ./cache/cord-302855-wwg6x1df.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320302140
doi: 10.1016/j.jinf.2020.04.006
summary:
  • Among cancer patients with COVID-19, the numbers of neutrophil, NLR(ratio of neutrophil to lymphocyte, IL-6, LDH and PCT in the severe/critical group were significantly higher than those in the mild group. In our study, the infection rate of COVID-19 among cancer patients in the single center was estimated to be 2.7% (37 of 1380 patients), which was 6 times higher than that in Wuhan until Mar 30, 2020 (0.45%, 50,006 of 11,081,000). In terms of the results of laboratory tests, we interestingly found that the numbers of neutrophil, NLR, IL-6, LDH and PCT ( Table 2 ) in the severe/critical group were significantly higher than those in the mild group. Cancer patients had a high infection rate of SARS-CoV-2 and were easy to become severe or critical cases, which should be monitored closely during the COVID-19 epidemic. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China

title:
  Clinical characteristics and prognosis in cancer patients with COVID-19: A single center''s retrospective study

abstract:
  • We describe the demographics, clinical characteristics, and prognosis of cancer patients with COVID-19 infection. • Cancer patients had a high infection rate of SARS-CoV-2 and were easy to become severe or critical cases. • Among cancer patients with COVID-19, the numbers of neutrophil, NLR(ratio of neutrophil to lymphocyte, IL-6, LDH and PCT in the severe/critical group were significantly higher than those in the mild group.


id: cord-303763-2784hze3
title: Risk factors for pandemic H1N1 2009 infection in healthcare personnel of four general hospitals
author: Choi, Seong-Ho
date: 2011-05-01
url: https://www.sciencedirect.com/science/article/pii/S0163445311001186
doi: 10.1016/j.jinf.2011.04.009
abstract:
  To characterize an outbreak of pandemic H1N1 2009 among healthcare personnel (HCP), we conducted a cross-sectional survey of HCP who had worked in four general hospitals during the outbreak. More than one-quarter of responding HCP (27.6%) had influenza-like illness (ILI) during the outbreak. The estimated infection rate of pandemic H1N1 2009 was 9.1% in the study of HCP. Independent risk factors for ILI were female gender, <40 years of age, the presence of chronic diseases associated with influenza complications, having family members with ILI or pandemic H1N1 2009, and working in influenza outpatient, influenza inpatient, non-influenza outpatient or emergency departments. During the outbreak of pandemic H1N1 2009, HCP frequently had ILI or the influenza infection. The development of the influenza infection in HCP was associated with some of their baseline characteristics, occupational risk factors, and non-occupational ones during the outbreak.


id: cord-303904-8ubm0kig
author: Verhagen, Lilly M.
date: 2013-06-22
url: https://www.sciencedirect.com/science/article/pii/S0163445313001588
doi: 10.1016/j.jinf.2013.06.010
title:
  Respiratory infections in Eñepa Amerindians are related to malnutrition and Streptococcus pneumoniae carriage

abstract:
  OBJECTIVES: High acute respiratory tract infection (ARTI) rates are observed in indigenous populations. We assessed the role of viral infections and nasopharyngeal bacterial carriage in ARTIs in Eñepa Amerindians from Venezuela. METHODS: In 40 children aged 0–10 years with ARTIs, healthy nearest-age sibling controls and their mothers the presence of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Mycoplasma pneumoniae, Chlamydophila pneumoniae/psittachi and 15 respiratory viruses was investigated. RESULTS: S. pneumoniae was the most frequently detected pathogen, with carriage rates of 75% and 38% in children and mothers respectively. In children, S. pneumoniae carriage was associated with ARTI risk in multivariate analysis (OR 14.1, 95% CI 1.4–137.7). Viral infections were not associated with ARTI risk. S. pneumoniae carriage was common in children of all ages while viral co-infections were more frequently present in children under 4 years compared to older children (46% vs. 17%, p < 0.01). An increase of one unit height-for-age Z score (i.e. improved chronic nutritional status) was associated with decreased odds of S. pneumoniae colonization in multivariate analysis (OR 0.66, 95% CI 0.44–0.99). CONCLUSIONS: In Eñepa children high S. pneumoniae carriage rates associated with a poor nutritional status contribute to the development of ARTIs.


id: cord-304176-yloqrblw
title: Prescribing COVID-19 treatments: what we should never forget
author: Tunesi, S.
date: 2020-05-13
txt: ./txt/cord-304176-yloqrblw.txt
cache: ./cache/cord-304176-yloqrblw.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.05.018
doi: 10.1016/j.jinf.2020.05.018
abstract: nan
summary:
  authors: Tunesi, S.; Bourgarit, A. COVID-19-induced proinflammatory status looks to trigger most severe SARS-CoV-2 forms (2). Many drugs have been hypothesized to be directly active against COVID-19 only because of a supposed antiviral activity: remdesivir, a molecule originally tested against Ebola virus, shows in vivo activity against MERS-CoV (5) but there is actually no real evidence of in vivo activity against COVID-19; lopinavir/ritonavir, a well-known protease inhibitor used in HIV treatment, has been widely used before randomized clinical trials showed his inefficacy in mortality reduction (6); chloroquine and hydroxychloroquine, which are largely used in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) treatment, show modest antiviral effects, but mortality due to QT elongation-related cardiac events is a matter of concern (7). Conversely, preliminary data about a potential role of ACE inhibitors in favouring the onset of severe forms of SARS-CoV-2 infection induced a massive change in antihypertensive drugs prescription that caused the onset of severe cardiovascular events (9).


id: cord-304787-fohgekp4
author: Prazuck, Thierry
date: 2020-06-29
url: https://api.elsevier.com/content/article/pii/S0163445320304485
doi: 10.1016/j.jinf.2020.06.066
abstract: nan
title:
  Investigation of a family outbreak of COVID-19 using systematic rapid diagnostic tests raises new questions about transmission


id: cord-305330-mklkugj5
title: Cancer in intensive care unit patients with COVID-19
author: Moiseev, Sergey
date: 2020-05-28
txt: ./txt/cord-305330-mklkugj5.txt
cache: ./cache/cord-305330-mklkugj5.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320303273?v=s5
doi: 10.1016/j.jinf.2020.05.053
abstract: nan
summary:
  susceptible to severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection and complications, although data on COVID-19 and malignancies remain limited. noted that patients with cancer were more likely to experience severe sequelae of SARS-CoV-2 infection, such as intensive care admission, invasive ventilation or death. 2 However, Wang and Zhang argued that the most important morbidity factor is exposure to an infection source, whereas worse outcomes from SARS-CoV-2 infection could be associated (at least partly) with older age of patients with cancer 3 . In a nationwide study, we evaluated the prevalence of malignancies among 1307 intensive care unit (ICU) patients with SARS-CoV-2 pneumonia who required respiratory support. However, our data suggest that other factors, such as older age and comorbidities, contribute significantly to the more severe course of SARS-CoV-2 infection in cancer patients.


id: cord-305462-2wz1f6k6
title: Respiratory viral infections in patients with chronic, obstructive pulmonary disease
author: Beckham, J. David
date: 2004-09-22
txt: ./txt/cord-305462-2wz1f6k6.txt
cache: ./cache/cord-305462-2wz1f6k6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15845430/
doi: 10.1016/j.jinf.2004.07.011
summary:
  OBJECTIVES: The purpose of the present study was to apply reverse transcription-PCR (RT-PCR) assays to clinical specimens collected from patients with acute respiratory illness and chronic obstructive pulmonary disease (COPD). METHODS: One hundred and ninety-four samples from two different study cohorts were analysed using RT-PCR assays for picornaviruses, coronaviruses 229E and OC43, influenza A and B viruses, respiratory syncytial virus, parainfluenza types 1–3 viruses, and human metapneumovirus and a PCR assay for adenoviruses. 11 The number of respiratory viral infections identified in asthmatic patients with acute exacerbations of disease increase significantly when RT-PCR assays are used in addition to other diagnostic methods. 3 In order to extend our understanding of the prevalence of respiratory viral infection in acute respiratory illnesses in patients with COPD, we used RT-PCR assays to evaluate samples from the previous two prospective studies for evidence of respiratory virus infection.

abstract:
  OBJECTIVES: The purpose of the present study was to apply reverse transcription-PCR (RT-PCR) assays to clinical specimens collected from patients with acute respiratory illness and chronic obstructive pulmonary disease (COPD). METHODS: One hundred and ninety-four samples from two different study cohorts were analysed using RT-PCR assays for picornaviruses, coronaviruses 229E and OC43, influenza A and B viruses, respiratory syncytial virus, parainfluenza types 1–3 viruses, and human metapneumovirus and a PCR assay for adenoviruses. The results were added to results obtained previously using cell culture and serologic methods. RESULTS: RT-PCR assays identified an additional 35 respiratory virus-associated illnesses not identified previously by cell culture or serology (n=46). Picornaviruses and coronaviruses were the most common viral infections identified only by RT-PCR. Overall, 41.8% of the acute respiratory illnesses evaluated were associated with a respiratory virus infection, with picornaviruses, coronaviruses and influenza viruses being the most common infections recognized. No human metapneumovirus infections were identified by RT-PCR assay. CONCLUSIONS: Respiratory viral infections are commonly associated with acute respiratory illness in COPD patients, and the use of RT-PCR assays significantly increases the ability to diagnose these infections.


id: cord-305583-p2jp5fiq
title: UK malaria treatment guidelines 2016
author: Lalloo, David G.
date: 2016-02-12
txt: ./txt/cord-305583-p2jp5fiq.txt
cache: ./cache/cord-305583-p2jp5fiq.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445316000475
doi: 10.1016/j.jinf.2016.02.001
summary:
  Severe falciparum malaria, or infections complicated by a relatively high parasite count (more than 2% of red blood cells parasitized) should be treated with intravenous therapy until the patient is well enough to continue with oral treatment. Severe falciparum malaria, or infections complicated by a relatively high parasite count (more than 2% of red blood cells parasitized) should be treated with intravenous therapy until the patient is well enough to continue with oral treatment. There are now three main therapeutic options for the treatment of uncomplicated falciparum malaria in adults in the UK: artemisinin combination therapy (ACT), oral atovaquoneeproguanil or quinine plus doxycycline (or quinine plus clindamycin in certain circumstances) (see Box 4 for details of doses). 52 In line with the WHO guidelines, we recommend that IV artesunate should be used preferentially over quinine as the drug of choice for treatment of severe falciparum malaria in children (grade 1A).

abstract:
  1.Malaria is the tropical disease most commonly imported into the UK, with 1300–1800 cases reported each year, and 2–11 deaths. 2. Approximately three quarters of reported malaria cases in the UK are caused by Plasmodium falciparum, which is capable of invading a high proportion of red blood cells and rapidly leading to severe or life-threatening multi-organ disease. 3. Most non-falciparum malaria cases are caused by Plasmodium vivax; a few cases are caused by the other species of plasmodium: Plasmodium ovale, Plasmodium malariae or Plasmodium knowlesi. 4. Mixed infections with more than one species of parasite can occur; they commonly involve P. falciparum with the attendant risks of severe malaria. 5. There are no typical clinical features of malaria; even fever is not invariably present. Malaria in children (and sometimes in adults) may present with misleading symptoms such as gastrointestinal features, sore throat or lower respiratory complaints. 6. A diagnosis of malaria must always be sought in a feverish or sick child or adult who has visited malaria-endemic areas. Specific country information on malaria can be found at http://travelhealthpro.org.uk/. P. falciparum infection rarely presents more than six months after exposure but presentation of other species can occur more than a year after exposure. 7. Management of malaria depends on awareness of the diagnosis and on performing the correct diagnostic tests: the diagnosis cannot be excluded until more than one blood specimen has been examined. Other travel related infections, especially viral haemorrhagic fevers, should also be considered. 8. The optimum diagnostic procedure is examination of thick and thin blood films by an expert to detect and speciate the malarial parasites. P. falciparum and P. vivax (depending upon the product) malaria can be diagnosed almost as accurately using rapid diagnostic tests (RDTs) which detect plasmodial antigens. RDTs for other Plasmodium species are not as reliable. 9. Most patients treated for P. falciparum malaria should be admitted to hospital for at least 24 h as patients can deteriorate suddenly, especially early in the course of treatment. In specialised units seeing large numbers of patients, outpatient treatment may be considered if specific protocols for patient selection and follow up are in place. 10. Uncomplicated P. falciparum malaria should be treated with an artemisinin combination therapy (Grade 1A). Artemether–lumefantrine (Riamet(®)) is the drug of choice (Grade 2C) and dihydroartemisinin-piperaquine (Eurartesim(®)) is an alternative. Quinine or atovaquone–proguanil (Malarone(®)) can be used if an ACT is not available. Quinine is highly effective but poorly-tolerated in prolonged treatment and should be used in combination with an additional drug, usually oral doxycycline. 11. Severe falciparum malaria, or infections complicated by a relatively high parasite count (more than 2% of red blood cells parasitized) should be treated with intravenous therapy until the patient is well enough to continue with oral treatment. Severe malaria is a rare complication of P. vivax or P. knowlesi infection and also requires parenteral therapy. 12. The treatment of choice for severe or complicated malaria in adults and children is intravenous artesunate (Grade 1A). Intravenous artesunate is unlicensed in the EU but is available in many centres. The alternative is intravenous quinine, which should be started immediately if artesunate is not available (Grade 1A). Patients treated with intravenous quinine require careful monitoring for hypoglycemia. 13. Patients with severe or complicated malaria should be managed in a high-dependency or intensive care environment. They may require haemodynamic support and management of: acute respiratory distress syndrome, disseminated intravascular coagulation, acute kidney injury, seizures, and severe intercurrent infections including Gram-negative bacteraemia/septicaemia. 14. Children with severe malaria should also be treated with empirical broad spectrum antibiotics until bacterial infection can be excluded (Grade 1B). 15. Haemolysis occurs in approximately 10–15% patients following intravenous artesunate treatment. Haemoglobin concentrations should be checked approximately 14 days following treatment in those treated with IV artemisinins (Grade 2C). 16. Falciparum malaria in pregnancy is more likely to be complicated: the placenta contains high levels of parasites, stillbirth or early delivery may occur and diagnosis can be difficult if parasites are concentrated in the placenta and scanty in the blood. 17. Uncomplicated falciparum malaria in the second and third trimester of pregnancy should be treated with artemether–lumefantrine (Grade 2B). Uncomplicated falciparum malaria in the first trimester of pregnancy should usually be treated with quinine and clindamycin but specialist advice should be sought. Severe malaria in any trimester of pregnancy should be treated as for any other patient with artesunate preferred over quinine (Grade 1C). 18. Children with uncomplicated malaria should be treated with an ACT (artemether–lumefantrine or dihydroartemisinin-piperaquine) as first line treatment (Grade 1A). Quinine with doxycycline or clindamycin, or atovaquone–proguanil at appropriate doses for weight can also be used. Doxycycline should not be given to children under 12 years. 19. Either an oral ACT or chloroquine can be used for the treatment of non-falciparum malaria. An oral ACT is preferred for a mixed infection, if there is uncertainty about the infecting species, or for P. vivax infection from areas where chloroquine resistance is common (Grade 1B). 20. Dormant parasites (hypnozoites) persist in the liver after treatment of P. vivax or P. ovale infection: the only currently effective drug for eradication of hypnozoites is primaquine (1A). Primaquine is more effective at preventing relapse if taken at the same time as chloroquine (Grade 1C). 21. Primaquine should be avoided or given with caution under expert supervision in patients with Glucose-6-phosphate dehydrogenase deficiency (G6PD), in whom it may cause severe haemolysis. 22. Primaquine (for eradication of P. vivax or P. ovale hypnozoites) is contraindicated in pregnancy and when breastfeeding (until the G6PD status of child is known); after initial treatment for these infections a pregnant woman should take weekly chloroquine prophylaxis until after delivery or cessation of breastfeeding when hypnozoite eradication can be considered. 23. An acute attack of malaria does not confer protection from future attacks: individuals who have had malaria should take effective anti-mosquito precautions and chemoprophylaxis during future visits to endemic areas.


id: cord-307333-n6jc0jy3
title: Interferon lambda 1–3 expression in infants hospitalized for RSV or HRV associated bronchiolitis
author: Selvaggi, Carla
date: 2014-01-02
txt: ./txt/cord-307333-n6jc0jy3.txt
cache: ./cache/cord-307333-n6jc0jy3.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S016344531300399X
doi: 10.1016/j.jinf.2013.12.010
summary:
  OBJECTIVES: The airway expression of type III interferons (IFNs) was evaluated in infants hospitalized for respiratory syncytial virus (RSV) or rhinovirus (HRV) bronchiolitis. KEYWORDS IFN lambda; IL-28; IL-29; RSV; HRV; MxA; ISG56; Viral load; Bronchiolitis Summary Objectives: The airway expression of type III interferons (IFNs) was evaluated in infants hospitalized for respiratory syncytial virus (RSV) or rhinovirus (HRV) bronchiolitis. Therefore, we evaluated whether there was a difference in the gene expression of IFN lambda 1e3 subtypes between infants with a clinical diagnosis of RSV associated acute bronchiolitis and those with HRV infection. Results demonstrated that in cells collected from nasopharyngeal washings of RSV positive infants there are higher mRNA levels of type III IFNs compared to those observed in infants with Figure 1 Gene expression of IFN lambda 1e3 during RSV or HRV bronchiolitis.

abstract:
  OBJECTIVES: The airway expression of type III interferons (IFNs) was evaluated in infants hospitalized for respiratory syncytial virus (RSV) or rhinovirus (HRV) bronchiolitis. As an additional objective we sought to determine whether a different expression of IFN lambda 1–3 was associated with different harboring viruses, the clinical course of bronchiolitis or with the levels of well established IFN stimulated genes (ISGs), such as mixovirus resistance A (MxA) and ISG56. METHODS: The analysis was undertaken in 118 infants with RSV or HRV bronchiolitis. Nasopharyngeal washes were collected for virological studies and molecular analysis of type III IFN responses. RESULTS: RSV elicited higher levels of IFN lambda subtypes when compared with HRV. A similar expression of type III IFN was found in RSVA or RSVB infected infants and in those infected with HRVA or HRVC viruses. Results also indicate that IFN lambda 1 and IFN lambda 2–3 levels were correlated with each other and with MxA and ISG56-mRNAs. In addition, a positive correlation exists between the IFN lambda1 levels and the clinical score index during RSV infection. In particular, higher IFN lambda 1 levels are associated to an increase of respiratory rate. CONCLUSIONS: These findings show that differences in the IFN lambda 1–3 levels in infants with RSV or HRV infections are present and that the expression of IFN lambda 1 correlates with the severity of RSV bronchiolitis.


id: cord-308501-z3eiac25
title: nBreastfeeding Risk from Detectable Severe Acute Respiratory Syndrome Coronavirus 2 in Breastmilk
author: Zhu, Chengliang
date: 2020-06-04
txt: ./txt/cord-308501-z3eiac25.txt
cache: ./cache/cord-308501-z3eiac25.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320303790?v=s5
doi: 10.1016/j.jinf.2020.06.001
abstract: nan
summary:
  An emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) pandemic, imposes a great threat to global public health 1 . The transmission and pathophysiology of SARS-CoV-2 gradually known among various populations, but public health effects of COVID-19 on women and their outcomes should not be ignored 1, 2 . In pregnant and perinatal women, vertical transmission of SARS-CoV-2 from infected mother to her newborn is a controversial issue [2] [3] [4] . Here, we represent clinical characteristics of COVID-19 pneumonia in puerperal women and evidence of SARS-CoV-2 shedding in her breastmilk. Possible Vertical Transmission of SARS-CoV-2 From an Infected Mother to Her Newborn Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records SARS-CoV-2 is not detectable in the vaginal fluid of women with severe COVID-19 infection.


id: cord-308852-qdn04pun
title: Household transmission of COVID-19-a systematic review and meta-analysis
author: Lei, Hao
date: 2020-08-25
txt: ./txt/cord-308852-qdn04pun.txt
cache: ./cache/cord-308852-qdn04pun.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.08.033
doi: 10.1016/j.jinf.2020.08.033
summary:
  title: Household transmission of COVID-19-a systematic review and meta-analysis • SARS-CoV-2 is much more transmissible than SARS-CoV and Middle East Respiratory Syndrome Coronavirus in households, which challenges the home isolation of COVID-19 patients. Here, we report a systematic review of household transmission studies of and try to assess the secondary attack rate of household COVID-19 transmission. Studies containing data on household transmission of COVID-19 were retrieved from the electronic databases: PubMed, Embase, and a Chinese database, China National Knowledge Infrastructure (CNKI) on 1 July, 2020. Case reports with only one family involved were also excluded for analysis, because the household transmissions event collection was biased towards infection caused more serious illness. Household secondary attack rate (SAR) was calculated as the number of identified cases divided by the number of household contacts. Household SAR were greater than SAR by other contacts (OR=10.72, 95% CI: 5.70-20.17, p<0.001), suggesting much higher rates of intra-family transmission of COVID-19.

abstract:
  • Infection risk of household contacts is 10 times higher than other contacts. • Risk of household transmission in adults is about 3-times higher than that in children. • SARS-CoV-2 is much more transmissible than SARS-CoV and Middle East Respiratory Syndrome Coronavirus in households, which challenges the home isolation of COVID-19 patients.


id: cord-309294-ax6sr3zr
author: Garrigues, Eve
date: 2020-08-25
txt: ./txt/cord-309294-ax6sr3zr.txt
cache: ./cache/cord-309294-ax6sr3zr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32853602/
doi: 10.1016/j.jinf.2020.08.029
abstract: nan
summary:
  title: Post-discharge persistent symptoms and health-related quality of life after hospitalization for COVID-19 1 However, only a few studies have assessed post-discharge persistent symptoms and health-related quality of life (HRQoL) after hospitalization for COVID-19. 2, 3 Here, we describe a single-centre study assessing post-discharge persistent symptoms and HRQoL of patients hospitalized in our COVID-19 ward unit more than 100 days after their admission. We designed a short phone questionnaire to collect post-discharge clinical symptoms, modified Medical Research Council (mMRC) dyspnoea scale scores, professional and physical activities, and attention, memory and/or sleep disorders. Comparisons between ward-and ICU patients led to no statistically significant differences regarding those symptoms. The present study shows that most patients requiring hospitalization for COVID-19 still have persistent symptoms, even 110 days after being discharged, especially fatigue and dyspnoea. Except pain or discomfort, we found no significant difference regarding persistent symptoms and HRQoL between ward patients versus ICU patients.

title:
  Post-discharge persistent symptoms and health-related quality of life after hospitalization for COVID-19


id: cord-309476-hel3h25h
author: Brown, Julianne R.
date: 2018-01-02
txt: ./txt/cord-309476-hel3h25h.txt
cache: ./cache/cord-309476-hel3h25h.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445317304139
doi: 10.1016/j.jinf.2017.12.014
summary:
  This included two cases of human parvovirus 4 (PARV4), 28 first described in 2005 when it was associated with a viraemic patient in whom an acute viral infection was suspected 49 ; one case of human coronavirus OC-43, 43 typically a human respiratory pathogen never previously described in a human case of encephalitis but known to cause encephalitis in mice 50 ; one case of human astrovirus MLB1, 46 of mumps vaccine virus in a child who was vaccinated prior to a primary immunodeficiency diagnosis. As with other molecular tests, including PCR which has become the gold standard of virological diagnostics, results from metagenomics applied to cases of encephalitis should be interpreted in the context of other clinical and laboratory findings, particularly when a novel or unexpected organism is detected.

title:
  Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases

abstract:
  BACKGROUND: Current estimates suggest that even in the most resourced settings, the aetiology of encephalitis is identified in less than half of clinical cases. It is acknowledged that filling this gap needs a combination of rigorous sampling and improved diagnostic technologies. Next generation sequencing (NGS) methods are powerful tools with the potential for comprehensive and unbiased detection of pathogens in clinical samples. We reviewed the use of this new technology for the diagnosis of suspected infectious encephalitis, and discuss the feasibility for introduction of NGS methods as a frontline diagnostic test. METHODS: A systematic literature review was performed, using MESH and text word searches for variants of “sequencing” and “encephalitis” in Medline and EMbase, and searching bibliographies and citations using the Web of Science database. Two authors independently reviewed, extracted and summarised data. FINDINGS: The review identified 25 articles reporting 44 case reports of patients with suspected encephalitis for whom NGS was used as a diagnostic tool. We present the data and highlight themes arising from these cases. There are no randomly controlled trials to assess the utility of NGS as a diagnostic tool. INTERPRETATION: There is increasing evidence of a role for NGS in the work-up of undiagnosed encephalitis. Lower costs and increasing accessibility of these technologies will facilitate larger studies of these patients. We recommend NGS should be considered as a front-line diagnostic test in chronic and recurring presentations and, given current sample-to-result turn-around times, as second-line in acute cases of encephalitis.


id: cord-309577-438fotfd
title: Dynamics of faecal SARS-CoV-2 in infected children during the convalescent phase
author: Xing, Yuhan
date: 2020-04-10
txt: ./txt/cord-309577-438fotfd.txt
cache: ./cache/cord-309577-438fotfd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32283149/
doi: 10.1016/j.jinf.2020.03.049
abstract: nan
summary:
  1 We would like to share findings from our paediatric patients who were positive for nucleic acid testing for SARS-CoV-2 in stools up to 8-20 days after clearance of viral RNA in respiratory specimens. Surprisingly, we found SARS-CoV-2 remained detectable in faeces of paediatric patients for approximately 4 weeks, whereas negative conversion of viral RNA in respiratory specimens occurred within 2 weeks after disease onset. Two children showed negative results for faecal detection of SARS-CoV-2 20 days after clear-ance of viral RNA in the respiratory tract, while another child persistently tested positive on faecal samples even 8 days after respiratory samples turning negative. Faecal shedding of viral RNA has been constantly reported in patients infected with SARS-CoV-2. 7 -10 One study reported over half of the 17 patients had faecal samples positive for SARS-CoV-2 detection, although virus copies in stools were less than those in respiratory specimens.


id: cord-310001-qng7h5cj
author: Tomlins, Jennifer
date: 2020-04-27
txt: ./txt/cord-310001-qng7h5cj.txt
cache: ./cache/cord-310001-qng7h5cj.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320302322
doi: 10.1016/j.jinf.2020.04.020
abstract: nan
summary:
  title: Clinical features of 95 sequential hospitalised patients with novel coronavirus 2019 disease (COVID-19), the first UK cohort Clinical features of 95 sequential hospitalised patients with novel coronavirus 2019 disease (COVID-19), the first UK cohort. Sir, Wang and colleagues recently reported in this journal the characteristics and prognostic factors of novel coronavirus 2019 (COVID-19) disease in 339 patients over 60 years of age presenting to Renmin Hospital of Wuhan University in Wuhan, China 1 . Numerous other case series of hospitalised patients in China have provided valuable insight into the clinical features of disease, risk factors for severity and case fatality rate. It is anticipated that age and the frequency of coexisting comorbidities in the UK population are likely to be strong drivers of outcome of and mortality in patients hospitalised with COVID-19 disease. We found a much higher median age and case fatality rate than that reported by other studies of all hospitalised patients with COVID-19.

title:
  Clinical features of 95 sequential hospitalised patients with novel coronavirus 2019 disease (COVID-19), the first UK cohort


id: cord-311766-m9yv4qkm
author: Demey, Baptiste
date: 2020-05-07
txt: ./txt/cord-311766-m9yv4qkm.txt
cache: ./cache/cord-311766-m9yv4qkm.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320302449
doi: 10.1016/j.jinf.2020.04.033
summary:
  Thus, the objective of our study was to evaluate four immunochromatographic assays for the detection of IgM and IgG antibodies to SARS-CoV-2 and to evaluate the kinetics of their detection by these LFA. We evaluated 4 immunochromatographic tests for the detection of IgM and IgG directed against SARS-CoV-2 ( Figure 1 ). Longitudinal immunochromatographic testing in all patients shows heterogeneity in the time to detection of antibodies after symptom reporting (Figure 2 ). With either IgM or IgG detection for a patient on days 5, 10 and 15 since onset of symptom, we calculated a clinical sensitivity between 9 and 24%, 67 and 82% and 100% respectively ( Figure 3B and Table 1 ). In conclusion, we described the kinetics of detection of post-symptom antibodies in 22 patients using immunochromatographic rapid tests and demonstrated the good performance of these tests for the detection of antibodies after SARS-CoV-2 infection.

title:
  Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays

abstract:
  In order to fight the SARS-CoV-2 pandemic infection, there is a growing need and demand for diagnostic tools that are complementary and different from the RT-PCR currently in use. Multiple serological tests are or will be very soon available but need to be evaluated and validated. We have thus tested 4 immunochromatographic tests for the detection of antibodies to SARS-CoV-2. In addition, we assessed the kinetics of antibody appearance using these assays in 22 patients after they were tested positive by RT-PCR. We observed great heterogeneity in antiboy detection post-symptom onset. The median antibody detection time was between 8 and 10 days according to the manufacturers. All the tests showed a sensitivity of 60 to 80% on day 10 and 100% on day 15. In addition, a single cross-reaction was observed with other human coronavirus infections. Thus, immunochromatographic tests for the detection of anti-SARS-CoV-2 antibodies may have their place for the diagnostic panel of COVID-19.


id: cord-311853-k6efd9vg
title: Decline in pneumococcal disease incidence in the time of COVID-19 in Singapore
author: Lim, Rachel HF
date: 2020-08-15
txt: ./txt/cord-311853-k6efd9vg.txt
cache: ./cache/cord-311853-k6efd9vg.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320305545?v=s5
doi: 10.1016/j.jinf.2020.08.020
abstract: nan
summary:
  Chow et al reported a marked decline in influenza incidence in Singapore during the first four months of 2020, likely attributable to public health measures aimed at controlling the coronavirus disease 2019 (COVID-19) pandemic (1) . As part of routine infectious disease surveillance for these institutions, we reviewed the results of all urinary streptococcal antigen tests performed, as well as the number of notifications submitted to the Ministry of Health for invasive pneumococcal disease (IPD) (a notifiable disease for which reporting is mandatory for all clinicians and clinical laboratories), from the years 2010 to 2020. We postulate that the public health COVID-19 prevention measures introduced in Singapore resulted in an inadvertent decrease in pneumococcal disease transmission. In conclusion, we observed a decreased incidence of pneumococcal disease at our institution that corresponded with the time period when public health measures were implemented to control COVID-19, suggesting that these measures had also had an inadvertent effect on the transmission of S.


id: cord-312602-855n5av1
author: Chen, Min
date: 2020-06-23
txt: ./txt/cord-312602-855n5av1.txt
cache: ./cache/cord-312602-855n5av1.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320304217
doi: 10.1016/j.jinf.2020.06.040
summary:
  title: Molecular identification of Cryptococcus gattii from cerebrospinal fluid using single-cell sequencing: a case study Comparing the sequence obtained from single-cell sequencing with the reference database, it was found that the infection was caused by Cryptococcus gattii sensu stricto (AFLP4/VGI genotype). Cryptococcal meningitis (CM) is a life-threatening fungal infection associated with the human central nervous system (CNS), which is mainly caused by yeasts of the basidiomycetous genus Cryptococcus, particularly species that belong to the Cryptococcus neoformans and Cryptococcus gattii complexes [5] . However, our case did not exhibit these clinical characteristics Notably, the scS technology in our study effectively and accurately generated enough sequence reads to facilitate direct detection and phylogenetic analysis of the cells of C. After further optimization of clinical sample separation, the scS technology will have great potential to accurately identify the etiologic agents of CNS-related mycoses, as well as other disease-causing fungal pathogens.

title:
  Molecular identification of Cryptococcus gattii from cerebrospinal fluid using single-cell sequencing: a case study

abstract:
  A 31-year-old man presented with cryptococcal meningitis (CM) without typical clinical characteristics, but with abnormal walking, difficult leg lifting and frequent falling. He was admitted to a hospital in Beijing for two months and then transferred to Peking Union Medical College Hospital. After multiple tests failed to identify the pathogen, single-cell sequencing (scS) was used to test the cerebrospinal fluid (CSF). Comparing the sequence obtained from single-cell sequencing with the reference database, it was found that the infection was caused by Cryptococcus gattii sensu stricto (AFLP4/VGI genotype). Cryptococcus is difficult to cultivate from complex body fluids. The etiological agent of this patient was identified and the patient was treated. This case is the first case in which scS was used to detect and identify fungal pathogen after conventional testing failed to identify the cause of the disease. This report demonstrates that the scS approach can be used to generate fungal genome sequences directly from the CSF of a CM patient. The scS technology could become a powerful tool to precise detect microscopically visible but uncultured pathogens in clinical samples.


id: cord-312984-rzryn3on
author: Pan, Daniel
date: 2020-09-19
txt: ./txt/cord-312984-rzryn3on.txt
cache: ./cache/cord-312984-rzryn3on.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S016344532030623X
doi: 10.1016/j.jinf.2020.09.016
abstract: nan
summary:
  title: Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity 8 From this small longitudinal cohort study on serially collected samples in acute COVID-19 cases of differing severity, we conclude that for symptomatic patients, it is difficult to obtain a ''false negative'' result on NPS, OPS, NS or CS samples, if sampled early (within 5 days) post-symptom onset, even if the swab was ''poorly'' taken. Despite a previous meta-analysis showing that sputum testing is possibly more sensitive for SARS-CoV-2 PCR testing, 9 other studies have shown that self-sampling from various URT sites performed satisfactorily for the diagnosis of acute COVID-19. Therefore, we further confirm that early (within 5 days of symptom onset), self-swabbed NPS, OPS, NS or CS samples for SARS-CoV-2 diagnostic testing in acute COVID-19 cases is a sensitive, practical approach, which reduces patient discomfort (as self-swabbing can be controlled) and minimises virus exposure to healthcare workers.

title:
  Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity


id: cord-315300-v3pxb997
title: CD4+T, CD8+T counts and severe COVID-19: A meta-analysis
author: Zhang, Haipeng
date: 2020-06-20
txt: ./txt/cord-315300-v3pxb997.txt
cache: ./cache/cord-315300-v3pxb997.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32569604/
doi: 10.1016/j.jinf.2020.06.036
abstract: nan
summary:
  A retrospective study by Liu et al was conducted to investigate the associated between lymphocyte subset counts and severe COVID-19 [1] . Therefore, we conducted this meta-analysis to investigate the relationship between CD4+T counts, CD8+T counts, CD4/CD8 ratio and the severity of COVID-19 patients. Trials providing data of counts of CD4+T, CD8+T or CD4/CD8 ratio in patients with non-severe or severe COVID-19 were included. It has been reported that low counts of CD4+T and CD8+T were associated with adverse outcome in patients with SARS, and the counts would rise dramatically when clinical symptoms improved [9] . Lymphocyte subset (CD4+, CD8+) counts reflect the severity of infection and predict the clinical outcomes in patients with COVID-19 Predictors of mortality for patients with COVID-19 pneumonia caused by SARS-CoV-2: a prospective cohort study


id: cord-315723-unhg20e9
title: Decline in invasive pneumococcal disease during COVID-19 pandemic in Taiwan
author: Juan, Hui-Chun
date: 2020-09-19
txt: ./txt/cord-315723-unhg20e9.txt
cache: ./cache/cord-315723-unhg20e9.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320306241
doi: 10.1016/j.jinf.2020.09.018
abstract: nan
summary:
  Dear Editor , We read with great interest Lim et al''s report, 1 which showed a decreased incidence of pneumococcal disease in Singapore during the first 27 weeks in 2020 in the time of COVID-19. Although the collateral benefit of controlling COVID-19 for other common respiratory infectious diseases, such as influenza and tuberculosis in Taiwan have been demonstrated, 2 , 3 the impact of the infection control and policy to prevent COVID-19 outbreak on pneumococcal disease remained unclear. Although many confounding factors, such as vaccine strategy or under-report of IPD during COVID-19 pandemic were not evaluated in this study, our findings was consistent with Singapore''s study 1 suggest that strictly performance of infection control and policy not only mitigate the threaten of COVID-19 but also reduce the burden of other respiratory infections disease -invasive pneumococcal diseases. Decline in pneumococcal disease incidence in the time of COVID-19 in Singapore


id: cord-316501-fl2wvhia
author: Noh, Ji Yun
date: 2020-05-21
txt: ./txt/cord-316501-fl2wvhia.txt
cache: ./cache/cord-316501-fl2wvhia.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320303108
doi: 10.1016/j.jinf.2020.05.035
summary:
  title: Asymptomatic infection and atypical manifestations of COVID-19: comparison of viral shedding duration • Among patients with COVID-19, 26.1% presented anosmia, and 22.6% complained of ageusia with median duration of 7 days. • Mean duration of SARS-CoV-2 viral shedding was 24.5 days. • Irrespective of clinical manifestations, all patients with COVID-19 showed prolonged viral shedding. to evaluate the prevalence of asymptomatic infection, anosmia (smell loss) and ageusia (taste 8 loss) among patients with mild COVID-19 in a residential treatment center (RTC). We also 9 compared the duration of SARS-CoV-2 viral shedding between groups with different clinical 10 manifestations. An observational cohort study was conducted for 199 patients with COVID-19 in a RTC at Rapid asymptomatic transmission of COVID-19 during 82 the incubation period demonstrating strong infectivity in a cluster of youngsters aged 16-83 23 years outside Wuhan and characteristics of young patients with COVID-19: A 84 prospective contact-tracing study

title:
  Asymptomatic infection and atypical manifestations of COVID-19: comparison of viral shedding duration

abstract:
  • More than 25% of patients with COVID-19 were asymptomatic. • Among patients with COVID-19, 26.1% presented anosmia, and 22.6% complained of ageusia with median duration of 7 days. • Mean duration of SARS-CoV-2 viral shedding was 24.5 days. • Irrespective of clinical manifestations, all patients with COVID-19 showed prolonged viral shedding.


id: cord-317315-yyssvbbl
title: Serial semiquantitative detection of SARS-CoV-2 in saliva samples
author: Mao, Ming-Hui
date: 2020-10-06
txt: ./txt/cord-317315-yyssvbbl.txt
cache: ./cache/cord-317315-yyssvbbl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33031835/
doi: 10.1016/j.jinf.2020.10.002
abstract: nan
summary:
  While the positive rates of nucleic acid detection from saliva, sputum, and oropharyngeal swab samples were significantly different at 3 and 6 weeks (see Appendix Table 3 ). The average time for nucleic acid detection results to become negative was 27.29±7.73 days for sputum samples, 27.82±12.09 days for oropharyngeal swab samples, and 24.53±13.59 days for saliva samples (see Appendix Table 4 ). Multivariate analysis found that clinical classification had a significant impact on the time of sputum and oropharyngeal swab samples to become negative (p=0.007, p=0.002) (see Appendix Table 5 ). The overall sensitivity, efficiency and specificity of saliva-sputum combined detection method were 93.40%, 94.00% and 95.20%, respectively (see Appendix Table 6 ). 1,5-9 total efficiency and specificity of the saliva detection method in this study were higher than those of the sputum and oropharyngeal swab detection methods (83.90% and 94.40%, respectively).


id: cord-317846-str9i01o
author: Chen, Dr. Xian
date: 2020-05-15
txt: ./txt/cord-317846-str9i01o.txt
cache: ./cache/cord-317846-str9i01o.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320302954
doi: 10.1016/j.jinf.2020.05.020
abstract: nan
summary:
  title: Mesenchymal stem cell therapy in severe COVID-19: a retrospective study of short-term treatment efficacy and side effects Therefore, diminishing the cytokine storm may be an important part of treatment in patients with severe COVID-19 [4] . On this basis, we conducted a retrospective study to evaluate the treatment efficacy and side effects of MSCs therapy on severe COVID-19. In our series, all the patients with severe COVID-19 survived and entered recovery after MSCs therapy, and only 3 patients experienced treatment side effects. Firstly, inflammation indexes, such as WBC counts and CRP were totally normal before MSCs therapy in most cases, which means that cytokine storm was mild to moderate and not serious in these cases. In conclusion, we suggested that MSCs therapy might be a promising option for the treatment of severe COVID-19, but should be used cautiously, especially in patients with metabolic acidosis or coronary heart disease.

title:
  Mesenchymal stem cell therapy in severe COVID-19: a retrospective study of short-term treatment efficacy and side effects


id: cord-318013-5om35tu8
title: The role of serology for COVID-19 control: Population, kinetics and test performance do matter
author: Marie, Tré-Hardy
date: 2020-05-15
txt: ./txt/cord-318013-5om35tu8.txt
cache: ./cache/cord-318013-5om35tu8.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320302978?v=s5
doi: 10.1016/j.jinf.2020.05.019
abstract: nan
summary:
  (1-4) The authors of these reports or correspondence highlighted the added value of serological testing, which, if captured within the correct timeframe after disease onset, can detect both active and past infections.(1) By providing estimates of who is and is not immune to SARS-CoV-2, serological data can be used to estimate epidemiological variables, such as the attack rate or case-fatality rate, which are necessary to assess how much community transmission has occurred and its burden.(5) They can also be used to strategically deploy immune health-care workers to reduce exposure of the virus to susceptible individuals or to assess the effect of non-pharmaceutical interventions at the population level and inform policy changes to release such measures. After two weeks, all tests demonstrate a sensitivity of 100%, as reported by other groups, (8, 10) except when the cut-off provided by the manufacturer were used for IgG detection (i.e. one of our 15 patients was never considered as positive).


id: cord-318126-gg68o52z
title: Observation and analysis of 26 cases of asymptomatic SARS-COV2 infection
author: Zhou, Juan
date: 2020-04-03
txt: ./txt/cord-318126-gg68o52z.txt
cache: ./cache/cord-318126-gg68o52z.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.03.028
doi: 10.1016/j.jinf.2020.03.028
abstract: nan
summary:
  We read with interest the article in this journal which revealed that CT scanning provides important bases for early diagnosis and treatment of COVID-19 (Corona Virus Infection Disease 2019) which is caused by SARS-COV2 (Severe Acute Respiratory Syndrome Coronavirus 2). We observed and analyzed the phenotypic characteristics of asymptomatic individuals originating from the active detection of high-risk individuals who had close contacts with COVID-19 patients during isolated observation with viral nucleic acid positive. A total of 26 cases of asymptomatic infection were detected as SARS-COV2 positive through swab specimen between January 20 to February 30. These data showed that people of different ages are generally susceptible to SARS-COV2, but the average age of asymptomatic patients is lower than the reported age of COVID-19 patients which was 40-70 years old (propinquity 73%). These cases proved that asymptomatic SARS-COV2 carriers can also spread the virus before the https://doi.org/10.1016/j.jinf.2020.03.028 0163-4453/© 2020 The British Infection Association.


id: cord-320826-o6ih2f23
author: Blairon, Laurent
date: 2020-07-31
txt: ./txt/cord-320826-o6ih2f23.txt
cache: ./cache/cord-320826-o6ih2f23.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320305144?v=s5
doi: 10.1016/j.jinf.2020.07.033
abstract: nan
summary:
  title: Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak We read with great interest the study of Chen Y et al., who analyzed, during the Chinese epidemic peak, the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 105 healthcare workers (HCWs) exposed to COVID-19 patients [1] . Our purpose was to document at the end of the Belgium epidemic the seroprevalence of SARS-CoV-2 in HCWs exposed to COVID-19 at varying degrees and to compare these rates with those observed by other teams worldwide. On the same day, all asymptomatic HCWs who agreed to participate benefited from both serological and RT-qPCR SARS-CoV-2 tests. High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients COVID-19 study: 8,4% of Belgian health workers have antibodies to SARS-COV-2 n

title:
  Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak


id: cord-321033-fusyx0t9
author: nan
date: 2020-05-27
txt: ./txt/cord-321033-fusyx0t9.txt
cache: ./cache/cord-321033-fusyx0t9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32473229/
doi: 10.1016/j.jinf.2020.05.040
abstract: nan
summary:
  3 Most patients surviving from ARDS caused by other coronaviruses like SARS-CoV and Middle East respiratory syndrome coronavirus suffered from impaired pulmonary function and radiological abnormalities. Arterial blood gas analysis (ABGA) reported impaired oxygenation of PaO2/FiO2 at 213 mmHg. The diagnostic RT-PCR on a nasopharyngeal swab specimen was positive for SARS-CoV-2 and a chest CT scan illustrated bilateral pneumonia ( Figure 1a ). On illness day 17, both oxygenation (PaO2/FiO2 348 mmHg) and chest CT significantly improved (Figure 1b) , and she was then weaned from mechanical ventilation. On illness day 12, he was transferred to the intensive care unit and converted to invasive mechanical ventilation because of worsening oxygenation (PaO2/FiO2 84 mmHg) and progressing abnormalities on chest CT scan with extensive ground-glass opacities and partial consolidation on bilateral lungs (Figure 2b ). Follow-up study on pulmonary function and lung radiographic changes in rehabilitating severe acute respiratory syndrome patients after discharge

title:
  Follow-up study on pulmonary function and radiological changes in critically ill patients with COVID-19


id: cord-321989-1enjopig
author: Li, Yanpeng
date: 2017-10-31
txt: ./txt/cord-321989-1enjopig.txt
cache: ./cache/cord-321989-1enjopig.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445317303420
doi: 10.1016/j.jinf.2017.10.012
summary:
  • We first present a HRV-C and HBoV1 co-infection in an adult woman with severe acute respiratory distress syndrome. • Our study suggests that HBoV1 co-infection might worsen the disease caused by HRV-C infection, and raises a question whether HRV-C-related severe pneumonia is often associated with co-infection of other respiratory viruses such as bocavirus. Dear Editor, Human rhinovirus (HRV) and bocavirus (HBoV) are two of the most common respiratory viruses associated with acute respiratory tract infections among children. A previous study reported a 16-month child who was infected by HBoV1 and also showed presence of HRV, developed severe pneumonia. 5 Here we reported co-infection with HBoV1 and HRV-C in an adult woman with acute respiratory distress syndrome (ARDS). In conclusion, our study reports a life-threatening pneumonia case caused by co-infection with HRV-C and HBoV1, and raises a question whether HRV-C-related severe pneumonia is often associated with co-infection of other respiratory viruses such as bocavirus.

title:
  Metagenomic analysis identified co-infection with human rhinovirus C and bocavirus 1 in an adult suffering from severe pneumonia

abstract:
  • We first present a HRV-C and HBoV1 co-infection in an adult woman with severe acute respiratory distress syndrome. • Our study suggests that HBoV1 co-infection might worsen the disease caused by HRV-C infection, and raises a question whether HRV-C-related severe pneumonia is often associated with co-infection of other respiratory viruses such as bocavirus.


id: cord-322451-cwpz4akv
title: Heroes of SARS: professional roles and ethics of health care workers
author: Hsin, Dena Hsin-Chen
date: 2004-07-27
txt: ./txt/cord-322451-cwpz4akv.txt
cache: ./cache/cord-322451-cwpz4akv.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445304001410
doi: 10.1016/j.jinf.2004.06.005
summary:
  To examine the professional moral duty of health care workers (HCWs) in the outbreak of severe acute respiratory syndrome (SARS) in 2003. In a number of countries in order to encourage HCW, the government and the public started to give the title of ''hero'' to nurses and doctors who are working in the frontline of SARS outbreak. While the ethical ideal of self-less sacrifice of life for curing disease is promoted in the public image and media, discussions with HCW in several countries suggests that being a hero is not what modern medical practice is for some HCWs. Most HCWs in Taiwan are working in the commercial hospital, where the hirer pushes them to focus their effort of work on business competition rather than the basic role of helpers to human''s health. Nurses'' professional care obligation and their attitudes towards SARS infection control measures in Taiwan during and after the 2003 epidemic

abstract:
  Objectives. To examine the professional moral duty of health care workers (HCWs) in the outbreak of severe acute respiratory syndrome (SARS) in 2003. Methods. Descriptive discussion of media reports, analysis of ethical principles and political decisions discussed in the outbreak, with particular emphasis on the events in mainland China and Taiwan. Results. There were differences in the way that Taiwan and mainland China responded to the SARS epidemic, however, both employed techniques of hospital quarantine. After early policy mistakes in both countries HCWs were called heroes. The label ‘hero’ may not be appropriate for the average HCW when faced with the SARS epidemic, although a number of self-less acts can be found. The label was also politically convenient. Conclusions. A middle ground for reasonable expectations from HCW when treating diseases that have serious risk of infection should be expected. While all should act according to the ethic of beneficence not all persons should be expected to be martyrs for society.


id: cord-322812-9u3ptqjs
author: Wells, Philippa M.
date: 2020-10-15
txt: ./txt/cord-322812-9u3ptqjs.txt
cache: ./cache/cord-322812-9u3ptqjs.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320306538
doi: 10.1016/j.jinf.2020.10.011
summary:
  METHODS: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. We undertook a population-based study of the humoral immune response to SARS-CoV-2, with regards to longitudinal clinical symptoms collected through a mobile phone app in a population-based sample of 431 TwinsUK volunteers. For three months prior to the visit, the majority of participants had completed regular logging of symptoms, via the C-19 Covid Symptom Study app 5 , enabling measurement of antibody response to COVID-19 with regards to clinical symptoms.

title:
  Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England

abstract:
  BACKGROUND: Understanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. METHODS: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. FINDINGS: We demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. INTERPRETATION: Seroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. FUNDING: NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC


id: cord-327246-idmo5ds7
author: M, Montero-Baladía
date: 2020-06-21
txt: ./txt/cord-327246-idmo5ds7.txt
cache: ./cache/cord-327246-idmo5ds7.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320303868
doi: 10.1016/j.jinf.2020.06.006
abstract: nan
summary:
  Current evidence suggests that systemic hyperinflammation and immune dysregulation play a key role in the development of severe lung and multiorgan damage found in critically ill COVID-19 patients 2, 3, 4 . Patients eligible for etoposide treatment were older than 18 years, presented biochemical alterations suggestive of severe hyperinflammation (ferritin levels >1000 ng/ml and/or IL-6 values >50 pg/ml), ARDS (defined by PaO 2 /FiO 2 < 300) and were not under mechanical ventilation. These preliminary results on 11 patients confirmed the safety and efficacy of etoposide as adjunctive salvage treatment for critically ill COVID-19 ARDS patients, exhibiting systemic hyperinflammation and previously treated with corticosteroids and interleukin inhibitors. In this preliminary experience, salvage treatment with etoposide in adjunction to immunosuppressants resulted in overall favorable outcome of a small cohort of severely ill COVID-19 ARDS patients presenting with systemic hyperinflammation.

title:
  Etoposide treatment adjunctive to immunosuppressants for critically ill COVID-19 patients: Etoposide for severe COVID-19 patients


id: cord-328068-qoz85x3r
title: The presence of Pneumocystis jirovecii in critically ill patients with COVID-19
author: Alanio, Alexandre
date: 2020-11-04
txt: ./txt/cord-328068-qoz85x3r.txt
cache: ./cache/cord-328068-qoz85x3r.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320306940?v=s5
doi: 10.1016/j.jinf.2020.10.034
abstract: nan
summary:
  title: The presence of Pneumocystis jirovecii in critically ill patients with COVID-19 3 Since pneumocystosis is usually reported in patients with T-cell immunodepression, 4 less attention has been paid to Pneumocystis jirovecii in non-immunocompromised ICU patients although it accounts for 7% of the co-infections reported in those admitted with Influenza. jirovecii acid nucleic detection in respiratory specimens sampled to identify co-infections in COVID-19 patients in the ICU. All consecutive patients admitted to the ICU between 2020/03/15 and 2020/05/01 with a positive SARS-CoV-2 PCR (Cobas ® SARS-CoV-2 Test, Roche, France) and ≥1 respiratory sample (bronchoalveolar lavage (BAL), tracheal aspirate, sputum) sent to the mycology department. jirovecii RTqPCR-negative patients, higher B-D-glucan concentrations (450 and 500pg/ml) lead to the diagnosis of pulmonary aspergillosis, another fungal infection of risk in COVID-19 patients. jirovecii-positive pulmonary samples is observed in critically ill COVID-19 patients. Diagnostic accuracy of serum (1-3)-β-D-glucan for Pneumocystis jirovecii pneumonia: a systematic review and meta-analysis


id: cord-328479-1tzysg7u
title: Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibodies in Pets in Wuhan, China
author: Chen, Jianjun
date: 2020-06-21
txt: ./txt/cord-328479-1tzysg7u.txt
cache: ./cache/cord-328479-1tzysg7u.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32579982/
doi: 10.1016/j.jinf.2020.06.045
abstract: nan
summary:
  In this study, we collected swab and blood samples from pet cats and dogs in Wuhan whose owners were confirmed to have COVID-19. Swab and whole blood samples were collected from 10 cats (four female, six male) and 9 dogs (four female, five male) (Supplementary Table 1 We then conducted telephone questionnaires with the owners of the three pets. In this study, we conducted a survey for SARS-CoV-2 in pets whose owners were diagnosed with COVID-19, in 15 communities in Wuhan. Prior to our study, a preprint of a research article posted online at bioRxiv indicated that SARS-CoV-2-specific antibodies were detected in cats in Wuhan at the time of the COVID-19 epidemic (7) . In addition, pet dogs and cats in Hong Kong (8), whose owners had been diagnosed with COVID-19, tested positive for SARS-CoV-2 RNA. Collectively, these results indicate the SARS-CoV-2 can be transmitted to companion animals, possible through contact with owners carrying COVID-19.


id: cord-330387-7lci44w5
author: Bird, Paul
date: 2020-06-18
txt: ./txt/cord-330387-7lci44w5.txt
cache: ./cache/cord-330387-7lci44w5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.06.035
doi: 10.1016/j.jinf.2020.06.035
abstract: nan
summary:
  title: High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads Similarly, another study from Leicester, UK compared hospitalised and community patient SARS-CoV-2 PCR (polymerase chain reaction) positivity rates with that of staff, 2 but again, did not assess which staff groups or clinical specialties were at most risk of acquiring COVID-19. In addition, we compared the SARS-CoV-2 PCR positivity rate against ethnicity for both the HCW and household contacts combined (Fig. 1C) . 8 We then compared the SARS-CoV-2 PCR positivity rates against various demographic parameters, ethnicity and symptom patterns in both the HCWs and household contacts (n=47, Table 1 ). In summary, we have compared the SARS-CoV-2 PCR positivity rates in this HCW and household contact cohort, across different clinical roles and specialties, ethnic groups, and explored the correlation between their symptom patterns and swab viral loads.

title:
  High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads


id: cord-331929-rot2vgso
title: REPLY TO: Interleukin-17: a potential therapeutic target in COVID-19
author: Piaserico, Stefano
date: 2020-06-29
txt: ./txt/cord-331929-rot2vgso.txt
cache: ./cache/cord-331929-rot2vgso.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320304448
doi: 10.1016/j.jinf.2020.06.063
abstract: nan
summary:
  As observed in the paper by Mendoza, IL-17 is thought to play a key role in the immune dysregulation observed in COVID-19 and in other severe coronavirus-mediated respiratory syndromes, therefore its inhibition has been suggested to determine a better outcome in these patients. IL-17 has been shown to exert direct pro-fibrotic effects on fibroblasts isolated from mouse and human lung through the activation of NF-kB, promoting production of TGF-β and expression of αsmooth muscle actin and eventually leading to collagen deposition 5 . Pulmonary fibrosis in SARS patients may be the result of the high inflammatory burden related not only to the anti-viral immune response, but also to ventilatorinduced lung injury (VILI). Moreover, anticoagulant therapies have been shown to ameliorate lung fibrosis in both murine models and human patients. In conclusion, IL-17 appears to be involved in several processes which might be relevant in the pathogenesis of COVID-19-induced pulmonary fibrosis.


id: cord-331931-2et3gcb5
title: Clinical and Imaging features of COVID-19 Patients: Analysis of Data from High-Altitude Areas
author: Zeng, Jie
date: 2020-04-08
txt: ./txt/cord-331931-2et3gcb5.txt
cache: ./cache/cord-331931-2et3gcb5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.03.026
doi: 10.1016/j.jinf.2020.03.026
abstract: nan
summary:
  title: Clinical and Imaging features of COVID-19 Patients: Analysis of Data from High-Altitude Areas This is the first report talking about the COVID-19 from high altitude areas. It is worth mentioning that a 77-years-old female patient had a history of tuberculosis, although only one lobe was involved with SARS-CoV-2, but still progresses to severe illness. There were 5 patients who had a negative initial CT scan but positive follow-up CT， which means that negative CT images cannot completely rule out COVID-19. In conclusion, this is the first report of COVID-19 in high altitude area in the world. Clinical characteristics and imaging manifestations of the 2019 novel coronavirus disease (COVID-19):A multi-center study in Wenzhou city Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study


id: cord-332786-7b6wz6i7
author: Ha, Dat P.
date: 2020-06-12
txt: ./txt/cord-332786-7b6wz6i7.txt
cache: ./cache/cord-332786-7b6wz6i7.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320303984
doi: 10.1016/j.jinf.2020.06.017
abstract: nan
summary:
  A recent report in this journal by Ibrahim and colleagues describing the potential binding interaction between SARS-CoV-2 spike protein and the host 78-kDa glucose regulated protein (GRP78) raised the possibility that GRP78 could be a facilitator for viral entry 1 and disruption of such interaction may be used to develop novel therapeutics specific against this virus 2 . In addition to its role in viral protein folding, GRP78 upregulation during viral replication could protect the virus-infected host cells from undergoing apoptosis since GRP78 is known to bind and maintain the ER-associated apoptotic machineries in their inactive forms and exert pro-survival effects especially under ER stress 3 . Conversely, the dependence of viruses on the ER and its key resident chaperone GRP78 for viral protein production and host cell survival could be the virus'' Achilles heel and offers a unique opportunity for combating SARS-CoV-2 and other virus infections.

title:
  The stress-inducible molecular chaperone GRP78 as potential therapeutic target for Coronavirus infection


id: cord-334443-3pyu8ucs
title: Public health might be endangered by possible prolonged discharge of SARS-CoV-2 in stool
author: He, Yu
date: 2020-03-05
txt: ./txt/cord-334443-3pyu8ucs.txt
cache: ./cache/cord-334443-3pyu8ucs.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.02.031
doi: 10.1016/j.jinf.2020.02.031
summary:
  According to a recent report, since December 8 2019, a novel identified coronavirus, SARS-CoV-2(previously named as 2019-nCOV) is causing outbreak of pneumonia in Wuhan, China and become the major concern throughout the world [1] . Those early reports may not represent actual rate of gastrointestinal symptoms caused by SARS-CoV-2, because in early stages of the outbreak, the limited resources for detection were only provided to those patients with severe symptoms like respiratory distress syndrome. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Detection and monitoring of SARS coronavirus in the plasma and peripheral blood lymphocytes of patients with severe acute respiratory syndrome

abstract:
  • The published data, which showed the COVID-19 patients with low digestive. • manifestation, might be misleading. Case with negative URT test showed positive in. • rectal scarab which challenge the isolation protocol. • As fomite transmission caused clusters of infection of SARS, adequate disinfection. • operations should be adopted in SARS-CoV-2 outbreak.


id: cord-335355-lcrbs2op
author: Kunutsor, Setor K.
date: 2020-05-28
txt: ./txt/cord-335355-lcrbs2op.txt
cache: ./cache/cord-335355-lcrbs2op.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S016344532030325X
doi: 10.1016/j.jinf.2020.05.045
abstract: nan
summary:
  In this context, we aimed to determine the nature of the relationships of admission levels of five main markers of liver injury (ALT, AST, gamma-glutamyltransferase (GGT), alkaline phosphatase (ALP) and total bilirubin) with the risk of clinical outcomes in patients with COVID-19 using a systematic meta-analysis. MEDLINE, Embase, and The Cochrane library were searched from 2019 to 17 May 2020 for published studies reporting on relationships between admission levels of markers of liver injury (GGT, ALT, AST, ALP and total bilirubin) and clinical outcomes in patients with COVID-19. Taking the overall evidence together, the data supports a higher prevalence of elevated admission levels of markers of liver injury in severe or mortality due to COVID-19 disease, which suggests that patients with elevated levels of liver markers at baseline (during admission) had higher risks of developing worse outcomes in COVID-19.

title:
  Markers of liver injury and clinical outcomes in COVID-19 patients: A systematic review and meta-analysis


id: cord-336591-a31oe7kc
author: Wong, Martin
date: 2020-06-21
txt: ./txt/cord-336591-a31oe7kc.txt
cache: ./cache/cord-336591-a31oe7kc.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320304266
doi: 10.1016/j.jinf.2020.06.044
abstract: nan
summary:
  We extracted the rate of increase in cumulative incidence for each country between 15 April to 30 April, 2020 from the COVID-19 data repository of the Johns Hopkins Centre for Systems Science and Engineering [3] . A linear regression model was constructed to examine the association between average stringency index and increase in incidence of COVID-19 cases as the outcome variable. The distribution of the Government response stringency index in various countries shows its increase over time (01 March, 2020 to 31, March 2020) [7] , probably due to the increase in incidence in this period. In multivariaable regression analysis of data in 139 countries (Table 1) , a higher stringency index was significantly associated with lower incidence increase between 15 The findings of this study showed that more stringent containment and control measures could potentially lead to better COVID-19 pandemic control.

title:
  Evaluation on different non-pharmaceutical interventions during COVID-19 pandemic: an analysis of 139 countries


id: cord-337557-ct43uoir
author: Guetl, Katharina
date: 2020-10-27
txt: ./txt/cord-337557-ct43uoir.txt
cache: ./cache/cord-337557-ct43uoir.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320306848
doi: 10.1016/j.jinf.2020.10.025
abstract: nan
summary:
  title: SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia (4, 5) Here, we report SARS-CoV-2 positive viral culture 7 weeks after onset of COVID-19 in a patient with an underlying immunosuppressive disorder, so-called X chromosome-linked agammaglobulinemia (XLA), demonstrating the potential of prolonged SARS-CoV-2 spreading beyond widely accepted isolation precautions. On April 15, five days after tocilizumab and convalescent plasma administration and five weeks after the initial diagnosis of COVID-19, SARS-CoV-2 RNA was not detectable for the first time. The patient showed progressive clinical recovery, but an alternating course of three negative followed by three positive SARS-CoV-2 RT-PCR results was subsequently observed. In summary, we have to assume that in our patient shedding of infectious SARS-CoV-2 stopped between week 7 and 10 of disease.

title:
  SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia


id: cord-337835-78i6j11i
author: Alfaraj, Sarah H.
date: 2017-02-09
txt: ./txt/cord-337835-78i6j11i.txt
cache: ./cache/cord-337835-78i6j11i.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445317300488
doi: 10.1016/j.jinf.2017.02.001
abstract: nan
summary:
  title: The impact of co-infection of influenza A virus on the severity of Middle East Respiratory Syndrome Coronavirus 1 We present four cases of combined infection with influenza and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection. A nasopharyngeal swab was positive for MERS-CoV with Ct value upE gene 37; ORF1A 36 and negative for Influenza. A nasopharyngeal swab was positive for MERS-CoV with Ct value upE gene 37; ORF1A 36 and negative for Influenza. A repeat swab after 3 days was negative for MERS-CoV but positive for influenza A. The NLST worked with the FES teams in the North West (NW) and West Midlands (WMids) regions of England to audit the reporting of Legionella cases with onset dates during each calendar year between 2012 and 2014, inclusive. WHO guidelines for investigation of cases of human infection with Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

title:
  The impact of co-infection of influenza A virus on the severity of Middle East Respiratory Syndrome Coronavirus


id: cord-337854-5ogip9tz
author: Huang, Wanqiu
date: 2020-07-02
txt: ./txt/cord-337854-5ogip9tz.txt
cache: ./cache/cord-337854-5ogip9tz.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320304564?v=s5
doi: 10.1016/j.jinf.2020.06.075
abstract: nan
summary:
  In our study, we developed an improved strategy, termed as nestRPA (nest recombinase polymerase amplification), which could greatly improve the sensitivity of nucleic acid detection for SARS-CoV-2 than RPA or qPCR. Using nestRPA technology, we found that positive plasmid containing SARS-CoV-2 with the concentration of 1 copy/ul could also be stably detected by Fragment 5 and nucleic acid detection results were negative using qPCR. Our results suggested that the ultra-sensitive nucleic acid detection technique has important implications for early identification of those asymptomatic carriers infected with SARS-CoV-2. In addition, many experts of COVID-19 prevention and treatment clearly pointed out that the inaccurate sample collection were also one of the important reasons for the false negative result of SARS-CoV-2 nucleic acid [6] [7] [8] . If all the links in the detection of SARS-CoV-2 nucleic acid could be strictly administrated, false negative could be completely eliminated, and the discontinuation of isolation will no longer be a dilemma for us.

title:
  The determination of release from isolation of COVID-19 patients requires ultra-high sensitivity nucleic acid test technology


id: cord-338333-yvm3d6xy
author: Tu, Danna
date: 2020-07-25
txt: ./txt/cord-338333-yvm3d6xy.txt
cache: ./cache/cord-338333-yvm3d6xy.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320305041
doi: 10.1016/j.jinf.2020.07.023
summary:
  title: Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 • Pediatric healthcare workers are at risk for SARS-CoV-2 transmission from children and aerosols increase SARS-CoV-2 infection rate. Here we would like to share our finding about the serum antibodies analyzed in a special group of pediatric medical workers exposed to varying levels of SARS-CoV-2 after Wuhan severe epidemic of COVID-19. The overall positive rate for SARS-CoV-2 IgG and IgM antibodies in the pediatric medical workers was 43.08 and 5.85%, respectively. This research revealed that pediatric medical workers are a high-risk group for infection by SARS-CoV-2, and the higher the exposure levels to COVID-19 patients and aerosol production, the greater chance of being infected. Table 1 Test results of serum antibodies in pediatric medical workers exposed to different levels of SARS-CoV-2 High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients

title:
  Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2

abstract:
  • Pediatric healthcare workers are at risk for SARS-CoV-2 transmission from children and aerosols increase SARS-CoV-2 infection rate. • ELISA and dual-target fluorescence accurately detect SARS-CoV-2 antibodies indicated that antibody detection should be considered as an auxiliary diagnosis of COVID-19. • Antibody positive subjects tested negative for SARS-CoV-2 neutralizing antibodies and SARS-CoV-2 antibodies diminish to near undetectable levels within two months.


id: cord-341754-rr7ei8o2
author: Aitken, Tess
date: 2020-05-08
txt: ./txt/cord-341754-rr7ei8o2.txt
cache: ./cache/cord-341754-rr7ei8o2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32437727/
doi: 10.1016/j.jinf.2020.05.001
abstract: nan
summary:
  title: Rethinking pandemic preparation: Global Health Security Index (GHSI) is predictive of COVID-19 burden, but in the opposite direction In the wake of the Ebola outbreak in 2014, the Global Health Security Index (GHSI) was developed with the aim of gauging countries'' capacity to deal with infectious disease outbreaks. 4 We analysed the association between GHSI and COVID-19 burden, represented by numbers of tests confirmed cases and deaths per million people per day since the first confirmed case in each country. Secondly, we used a generalised linear model (GLM) to determine the association between GHSI and confirmed cases and deaths per million people per day, with adjustment for testing rate, population median age and proportion of females. After adjusting for testing rate, median age and the proportion of females, a positive association was also observed between GHSI and COVID-19 cases and deaths, with the biggest burden borne by countries at the highest quartile of GHSI.

title:
  Rethinking pandemic preparation: Global Health Security Index (GHSI) is predictive of COVID-19 burden, but in the opposite direction


id: cord-346967-br4kpm6i
title: Acute hepatitis caused by asymptomatic COVID-19 infection
author: Bongiovanni, Marco
date: 2020-09-03
txt: ./txt/cord-346967-br4kpm6i.txt
cache: ./cache/cord-346967-br4kpm6i.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320305867
doi: 10.1016/j.jinf.2020.09.001
abstract: nan
summary:
  Acute liver injury at admission is a quite common finding in subjects affected by COVID-19 pneumonia (5) ; although the elevation of aminotransferases is usually mild, it seems associated with disease severity. In particular, it has been demonstrated that SARS-CoV-2 infection in the liver directly contributes to hepatic impairment in patients with COVID-19 pneumonia (6) . We report here the case of a young woman diagnosed with COVID-19 infection in absence of respiratory symptoms, presenting at the admission with significant elevation of liver function tests compatible with acute hepatitis. (8) described a non-icteric, acute hepatitis in an HIV-infected woman, but their patient developed overt respiratory symptoms in the hours immediately following diagnosis and also had other possible causes of liver tests abnormalities such as the use of concomitant drugs and a fair number of comorbidities. Mild-to moderate liver test abnormalities are becoming a frequent finding in subjects admitted to hospital for COVID-19 infection.


id: cord-347280-jpwf55l6
title: Laboratory characteristics of patients infected with the novel SARS-CoV-2 virus
author: Skevaki, Chrysanthi
date: 2020-06-21
txt: ./txt/cord-347280-jpwf55l6.txt
cache: ./cache/cord-347280-jpwf55l6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.06.039
doi: 10.1016/j.jinf.2020.06.039
summary:
  Furthermore, another study of 140 hospitalized patients in Wuhan, demonstrated significantly higher leukocyte counts among those with severe COVID-19 disease, compared to patients with milder infection (p=0.003) 3 . Absolute lymphopenia is commonly observed in patients with COVID-19, but pronounced lymphocyte depletion is a cardinal marker of enhanced disease severity and an indicator of imminent death, that has been consistently depicted by almost all currently published reports, coming mainly from China 1-7 . A retrospective Chinese study reported that NLR, along with the SARS-CoV-2 IgG levels, could be used as a simple discriminative tool for severity between COVID-19 patients, and further predict the clinical outcome of these patients 14 . Current data support that critically ill patients as well as fatal cases of COVID-19 have significantly higher LDH levels (usually >320 U/L) compared to moderate infections 1, 2, 5, 6, 11, 16 .

abstract:
  A subgroup of COVID-19 patients develop very severe disease with requirement for ICU treatment, ventilation, and ECMO therapy. Laboratory tests indicate that the immune and clotting system show marked alterations with hyper-activation, hyper-inflammation, cytokine storm development. Furthermore, organ-specific biomarkers demonstrate the involvement of cardiac muscle, kidney, and liver dysfunction in many patients. In this article the use of laboratory biomarkers is discussed with regard to their use for diagnosis, disease progression, and risk assessment.


id: cord-348129-tph0d5fl
author: De Deyn, Michelle Lee Zhi Qing
date: 2020-06-25
txt: ./txt/cord-348129-tph0d5fl.txt
cache: ./cache/cord-348129-tph0d5fl.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jinf.2020.06.058
doi: 10.1016/j.jinf.2020.06.058
abstract: nan
summary:
  Based on news reports and official press releases, it is evident that many Asian countries, which have successfully contained the first wave of infections, are now experiencing a second wave of imported cases from abroad and worsening local transmission 2 . After the 2003 severe acute respiratory syndrome-related coronavirus (SARS-CoV) outbreak, Singapore authorities had put in place a multi-ministry taskforce and a Disease Outbreak Response System Condition (DORSCON) framework that enables the whole-of-government to respond immediately to any disease outbreak and guide interventions 5 . While Hong Kong saw her first imported case on 22 January 2020 and had taken similar pre-emptive measures prior to this 6 . The role of community-wide wearing of face mask for control of coronavirus disease 2019 (COVID-19) epidemic due to SARS-CoV-2 Confirmed imported case of novel coronavirus infection in Singapore; multi-ministry taskforce ramps up precautionary measures

title:
  A tale of two cities: a comparison of Hong Kong and Singapore''s early strategies for the Coronavirus Disease 2019 (COVID-19)


id: cord-350159-i2ig6dtr
author: Daunt, Anna
date: 2020-06-21
txt: ./txt/cord-350159-i2ig6dtr.txt
cache: ./cache/cord-350159-i2ig6dtr.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320304308?v=s5
doi: 10.1016/j.jinf.2020.06.049
abstract: nan
summary:
  3 An adapted version of the risk score, with twelve variables, was used to predict clinical deterioration (i.e. death or admission to critical care) in a cohort of 1,157 confirmed COVID-19 patients in one London NHS Trust. However, how the score proposed by EAMS performs in front-line settings and its implications for how many patients will likely receive Remdesivir for COVID-19 is currently unknown. According to the EAMS score, 262 (75.3%) of the eligible patients in our cohort would have been classified as high-risk and 86 (24.7%%) as low-risk. While reassuring that the scoring system seems show reasonable performance in identifying most of those at high risk of adverse outcomes in our cohort, 11.3% of those who deteriorate and met inclusion criteria were missed by this score. A clinical risk score to identify patients with COVID-19 at high risk of critical care admission or death: an observational cohort study

title:
  Validity of the UK Early Access to Medicines Scheme Criteria for Remdesivir use in patients with COVID-19 disease


id: cord-350670-qk76szs0
title: Cardiac injury and mortality in COVID-19: a reappraisal
author: Vrsalovic, Mislav
date: 2020-06-30
txt: ./txt/cord-350670-qk76szs0.txt
cache: ./cache/cord-350670-qk76szs0.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0163445320304473
doi: 10.1016/j.jinf.2020.06.068
abstract: nan
summary:
  Based on the aforementioned methodological issues we performed an additional sub-analysis that included the two largest studies from Wuhan, China, which included 940 patients with COVID-19 (Table 1) , accounting for the fact that both studies analysed hospitalized cases with severe and critical illness. Meta-analysis of those studies that reported adjusted HR (using the generic inverse variance method and fixed effects model), showed a significant association between elevated troponin values and mortality (HR = 3.08; 95% CI 1.95 -4.87) (Fig. 1) , and no significant heterogeneity between studies was detected (Cochran Q = 0.44, p = 0.50). Cardiac injury and prognosis in covid-19: methodological considerations and updated meta-analysis Cardiac troponins predict mortality in patients with COVID-19: A meta-analysis of adjusted risk estimates Risk factors for severity and mortality in adult COVID-19 inpatients in Wuhan Characteristics and clinical significance of myocardial injury in patients with severe coronavirus disease


id: cord-352111-frk319q1
title: COVID-19 Follow up Testing
author: Woodruff, Amelita
date: 2020-05-11
txt: ./txt/cord-352111-frk319q1.txt
cache: ./cache/cord-352111-frk319q1.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320302899?v=s5
doi: 10.1016/j.jinf.2020.05.012
summary:
  • 70% of patients met CDC guidelines for release from quarantine & still tested (+); • The average time from onset of symptoms to negative testing was 19 days.  70% of patients met CDC guidelines for release from quarantine & still tested (+)  The average time from onset of symptoms to negative testing was 19 days Dear Editor, There is some uncertainty regarding the incubation period of the SARS-CoV-2 virus. The non-test-based strategy recommends that COVID-19 patients can discontinue self-isolation when they have been afebrile for 72 hours without anti-pyretic medications, have improvement in respiratory symptoms, and have at least 10 days elapse since symptoms started, recently increased from 7 days. The test-based strategy requires resolution of fever without the use of anti-pyretics, improvement of respiratory symptoms, and two consecutive negative COVID-19 nasopharyngeal swabs collected ≥24 hours apart. In our patient population, the average time from the onset of symptoms to negative testing is 19 days.

abstract:
  • Positive cases of SARS-CoV-2 were seen in the Mayo Clinic FL COVID Virtual Clinic. • 70% of patients met CDC guidelines for release from quarantine & still tested (+); • The average time from onset of symptoms to negative testing was 19 days.


id: cord-353608-de6rrf7v
author: Saito, Sho
date: 2020-11-02
txt: ./txt/cord-353608-de6rrf7v.txt
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url: https://doi.org/10.1016/j.jinf.2020.10.033
doi: 10.1016/j.jinf.2020.10.033
summary:
  Mortality (1.2% vs 7.3%) in hospitalized or discharged patients was also lower in the second wave; the same trend was observed on stratification according to age and severity at admission (Table 1 ). Our study showed that the proportion of cases involving severe disease at admission was smaller in the second wave. Data from the second wave indicated a demographic shift toward a younger population with fewer comorbidities, a lower proportion of severe patients at admission, and decreased mortality. However, the mortality was lower in second wave even if stratifying age and severity at admission. The findings of our study indicated that in the first wave, the medical system was under greater strain with more severe cases on admission. In the second wave, patients were younger with fewer underlying diseases and lower mortality rates. Risk factors associated with disease severity and length of hospital stay in COVID-19 patients

title:
  First and second COVID-19 waves in Japan: A comparison of disease severity and characteristics: Comparison of the two COVID-19 waves in Japan

abstract:
  • Coronavirus disease has emerged as a global pandemic. • Japan has experienced two waves of the disease. • The second wave had a lower proportion of severe cases on admission.


id: cord-354612-7f91l0n9
title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS
author: Villar, Livia Melo
date: 2020-07-23
txt: ./txt/cord-354612-7f91l0n9.txt
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mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0163445320304916?v=s5
doi: 10.1016/j.jinf.2020.07.017
abstract: nan
summary:
  title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS A total of four individuals (two hepatitis cases and two without liver disease) were negative to SARS CoV-2 in NPS and saliva (100% of specificity). Positive concordant results in NPS and saliva were observed in seven individuals (two hepatitis cases and 5 without liver disease) until 7 days after onset of symptoms (100% of sensitivity). This is the first report of SARS CoV-2 detection in saliva samples among liver disease patients showing best results until 7 days of beginning of symptoms. In addition, there is no information regarding the usefulness of saliva for detecting SARS CoV-2 RNA in individuals presenting comorbidities, such as liver disease. Since saliva can be collected easily, SARS CoV-2 RNA detection in saliva can be useful strategy to increase the access of sample collection for the diagnosis of COVID-19 in patients with liver disease.


