# ent

id: cord-267436-mivxm8oh
type: ORG
entity:
  1 World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis


id: cord-289744-suiqh3gv
type: ORG
entity:
  Service de Microbiologie Clinique des HUPSSD Service de Microbiologie Clinique des HUPSSD Service Pédiatrie Générale et


id: cord-320548-oigyut2k
type: ORG
entity:
  Asia Writing Committee of the World Health Organization Consultation on Northern Hemisphere Infl uenza Vaccine Composition


id: cord-332238-qw2ual51
type: ORG
entity:
  Letter to US Immigration and Customs Enforcement Office of Detention and Removal Office of Inspector General Concerns


id: cord-296573-4c9gch5b
type: DISEASE
entity:
  influenza A H5N1 a tale of two cities date 2013 08 19 journal Lancet Infect Dis DOI 10 1016 s1473 3099 13 70167 1 sha 0fa2f3fcf3b8a5fce92ea36064ca6a458c992503


id: cord-313615-cts45n3j
type: ORG
entity:
  Federal Emergency Management Agency USA Special Events Contingency Planning Job Aids Manual World Health Organization Writing Group Non


id: cord-273910-fna7s9te
type: GGP
entity:
  TRAF6 tumour necrosis factor receptor associated factor 6 SNP single nucleotide polymorphism γ D glutamyl


id: cord-303272-1w8epdht
type: CELL_LINE
entity:
  mammalian cell lines Human betacoronavirus 2c EMC 2012 related viruses in bats Ghana and Europe Genetic characterization of betacoronavirus lineage C viruses


id: cord-303272-1w8epdht
type: DISEASE
entity:
  human coronavirus OC43 antigen One cow and one goat serum reacted with human coronavirus OC43 antigen


id: cord-278256-dmrtsxik
type: ORG
entity:
  Ningbo Clinical Research Center for Children s Health and Diseases Project of Ningbo Reproductive Medicine Centre


# bib

id: cord-009476-4emc4o6n
title: Case definition and management of patients with MERS coronavirus in Saudi Arabia
author: Madani, Tariq A
date: 2014-09-22
txt: ./txt/cord-009476-4emc4o6n.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158994/
doi: 10.1016/s1473-3099(14)70918-1
abstract: nan
summary:
  16 outbreak and prevent human-to-human and animalto-human transmission; an appropriate management algorithm, including best-practice guidelines for accurate diagnosis, infection control, intensive care, emergency medicine, and treatment; prioritise research related to the MERS-CoV outbreak such as case-control and cohort studies, seroprevalence studies, and clinical trials; and to eff ectively monitor outbreak control activities. 2 The new case defi nition (appendix) was developed based on reported health-care-associated MERS-CoV pneumonia (added as category 2 in the new case defi nition) and non-respiratory characteristics of patients with confi rmed infection who fi rst presented with acute febrile dengue-like illness with body aches, leucopenia, and thrombocytopenia (added as category 3). WHO Revised interim case defi nition for reporting to WHO-Middle East respiratory syndrome coronavirus (MERS-CoV): as of First confi rmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in the United States, updated information on the epidemiology of MERS-CoV infection, and guidance for the public, clinicians, and Public Health Authorities


id: cord-011468-1ienwzy8
title: When does a major outbreak become a Public Health Emergency of International Concern?
author: Durrheim, David N
date: 2020-05-19
txt: ./txt/cord-011468-1ienwzy8.txt
cache: ./cache/cord-011468-1ienwzy8.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237181/
doi: 10.1016/s1473-3099(20)30401-1
abstract: nan
summary:
  The International Health Regulations 3 do not require actual international spread, only a high potential for that spread, and thus the criteria for a PHEIC had already been met by the second Emergency Committee meeting. Global health scholars have criticised the Emergency Committee process as lacking transparency, using "irrelevant considerations, undue influence and political interference", 5 and delaying declaration when International Health Regulations criteria have been met. 7 By the time the Emergency Committee declared a PHEIC for COVID-19 on Jan 30, 2020, 7736 cases and 179 deaths had been confirmed in mainland China, with 107 cases confirmed in 21 other countries. Level 1 PHEIC alert should indicate a high risk outbreak in a single country, with the potential for international spread requiring concerted public health efforts to contain and manage it locally. statement-on-the-meeting-of-theinternational-health-regulations-(2005)-emergency-committee-forebola-virus-disease-in-the-democratic-republic-of-the-congo


id: cord-254478-scc9wee0
author: To, Kelvin Kai-Wang
date: 2020-03-23
url: https://www.ncbi.nlm.nih.gov/pubmed/32213337/
doi: 10.1016/s1473-3099(20)30196-1
title:
  Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

abstract:
  BACKGROUND: Coronavirus disease 2019 (COVID-19) causes severe community and nosocomial outbreaks. Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available. Nasopharyngeal and throat swabs are usually obtained for serial viral load monitoring of respiratory infections but gathering these specimens can cause discomfort for patients and put health-care workers at risk. We aimed to ascertain the serial respiratory viral load of SARS-CoV-2 in posterior oropharyngeal (deep throat) saliva samples from patients with COVID-19, and serum antibody responses. METHODS: We did a cohort study at two hospitals in Hong Kong. We included patients with laboratory-confirmed COVID-19. We obtained samples of blood, urine, posterior oropharyngeal saliva, and rectal swabs. Serial viral load was ascertained by reverse transcriptase quantitative PCR (RT-qPCR). Antibody levels against the SARS-CoV-2 internal nucleoprotein (NP) and surface spike protein receptor binding domain (RBD) were measured using EIA. Whole-genome sequencing was done to identify possible mutations arising during infection. FINDINGS: Between Jan 22, 2020, and Feb 12, 2020, 30 patients were screened for inclusion, of whom 23 were included (median age 62 years [range 37–75]). The median viral load in posterior oropharyngeal saliva or other respiratory specimens at presentation was 5·2 log(10) copies per mL (IQR 4·1–7·0). Salivary viral load was highest during the first week after symptom onset and subsequently declined with time (slope −0·15, 95% CI −0·19 to −0·11; R(2)=0·71). In one patient, viral RNA was detected 25 days after symptom onset. Older age was correlated with higher viral load (Spearman's ρ=0·48, 95% CI 0·074–0·75; p=0·020). For 16 patients with serum samples available 14 days or longer after symptom onset, rates of seropositivity were 94% for anti-NP IgG (n=15), 88% for anti-NP IgM (n=14), 100% for anti-RBD IgG (n=16), and 94% for anti-RBD IgM (n=15). Anti-SARS-CoV-2-NP or anti-SARS-CoV-2-RBD IgG levels correlated with virus neutralisation titre (R(2)>0·9). No genome mutations were detected on serial samples. INTERPRETATION: Posterior oropharyngeal saliva samples are a non-invasive specimen more acceptable to patients and health-care workers. Unlike severe acute respiratory syndrome, patients with COVID-19 had the highest viral load near presentation, which could account for the fast-spreading nature of this epidemic. This finding emphasises the importance of stringent infection control and early use of potent antiviral agents, alone or in combination, for high-risk individuals. Serological assay can complement RT-qPCR for diagnosis. FUNDING: Richard and Carol Yu, May Tam Mak Mei Yin, The Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, and Sanming Project of Medicine.


id: cord-261133-m00gcci4
title: Understanding the symptoms of the common cold and influenza
author: Eccles, Ron
date: 2005-10-25
txt: ./txt/cord-261133-m00gcci4.txt
cache: ./cache/cord-261133-m00gcci4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16253889/
doi: 10.1016/s1473-3099(05)70270-x
summary:
  52 The mechanism of headache caused by cytokines is unknown but it is interesting that headache induced by cytokines is accompanied by symptoms such as fatigue, anorexia, malaise, nausea, and depression, and these symptoms are commonly associated with URTIs. A sensation of chilliness is an early symptom of common cold, 7 and is sometimes explained as an initial stage of fever, since vasoconstriction of skin blood vessels may cause a fall in skin temperature that is perceived as chilliness. 65 The cytokine stimulation of prostaglandin E2 production in skeletal muscle, and the effects of prostaglandin E2 on sensory nerves in muscle, may explain the myalgia associated with URTIs. In a study of common cold symptoms induced by challenge with infected nasal secretions, URTI symptoms were classified as either "early" or "later" symptoms.

abstract:
  The common cold and influenza (flu) are the most common syndromes of infection in human beings. These diseases are diagnosed on symptomatology, and treatments are mainly symptomatic, yet our understanding of the mechanisms that generate the familiar symptoms is poor compared with the amount of knowledge available on the molecular biology of the viruses involved. New knowledge of the effects of cytokines in human beings now helps to explain some of the symptoms of colds and flu that were previously in the realm of folklore rather than medicine—eg, fever, anorexia, malaise, chilliness, headache, and muscle aches and pains. The mechanisms of symptoms of sore throat, rhinorrhoea, sneezing, nasal congestion, cough, watery eyes, and sinus pain are discussed, since these mechanisms are not dealt with in any detail in standard medical textbooks.


id: cord-261533-73721b24
author: Mok, Chris Ka Pun
date: 2020-10-06
url: https://doi.org/10.1016/s1473-3099(20)30599-5
doi: 10.1016/s1473-3099(20)30599-5
title:
  T-cell responses to MERS coronavirus infection in people with occupational exposure to dromedary camels in Nigeria: an observational cohort study

abstract:
  BACKGROUND: Middle East respiratory syndrome (MERS) remains of global public health concern. Dromedary camels are the source of zoonotic infection. Over 70% of MERS coronavirus (MERS-CoV)-infected dromedaries are found in Africa but no zoonotic disease has been reported in Africa. We aimed to understand whether individuals with exposure to dromedaries in Africa had been infected by MERS-CoV. METHODS: Workers slaughtering dromedaries in an abattoir in Kano, Nigeria, were compared with abattoir workers without direct dromedary contact, non-abattoir workers from Kano, and controls from Guangzhou, China. Exposure to dromedaries was ascertained using a questionnaire. Serum and peripheral blood mononuclear cells (PBMCs) were tested for MERS-CoV specific neutralising antibody and T-cell responses. FINDINGS: None of the participants from Nigeria or Guangdong were MERS-CoV seropositive. 18 (30%) of 61 abattoir workers with exposure to dromedaries, but none of 20 abattoir workers without exposure (p=0·0042), ten non-abattoir workers or 24 controls from Guangzhou (p=0·0002) had evidence of MERS-CoV-specific CD4(+) or CD8(+) T cells in PBMC. T-cell responses to other endemic human coronaviruses (229E, OC43, HKU-1, and NL-63) were observed in all groups with no association with dromedary exposure. Drinking both unpasteurised camel milk and camel urine was significantly and negatively associated with T-cell positivity (odds ratio 0·07, 95% CI 0·01–0·54). INTERPRETATION: Zoonotic infection of dromedary-exposed individuals is taking place in Nigeria and suggests that the extent of MERS-CoV infections in Africa is underestimated. MERS-CoV could therefore adapt to human transmission in Africa rather than the Arabian Peninsula, where attention is currently focused. FUNDING: The National Science and Technology Major Project, National Institutes of Health.


id: cord-267436-mivxm8oh
title: Treatment and vaccines for severe acute respiratory syndrome
author: Groneberg, David A
date: 2005-03-10
txt: ./txt/cord-267436-mivxm8oh.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1473309905013071
doi: 10.1016/s1473-3099(05)01307-1
summary:
  The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. 31 The results of a randomised clinical study in Guangdong, involving multiple different treatment arms, suggest that ribavirin given at a low dose (400-600 mg/day) was less effective compared with an early and aggressive use of steroids with interferon alfa. Search terms were "severe acute respiratory syndrome", "SARS", "treatment", "coronavirus", "infection", "SARS coronavirus", "vaccination", and "antiviral". Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Generation and characterization of DNA vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus

abstract:
  The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002–2003 outbreak, is a coronavirus that was unknown before the outbreak. Although many different treatments were used during the outbreak, none were implemented in a controlled fashion. Thus, the optimal treatment for SARS is unknown. Since the outbreak, much work has been done testing new agents against SARS using in-vitro methods and animal models. In addition, global research efforts have focused on the development of vaccines against SARS. Efforts should be made to evaluate the most promising treatments and vaccines in controlled clinical trials, should another SARS outbreak occur.


id: cord-267476-j59tm40d
title: Connecting clusters of COVID-19: an epidemiological and serological investigation
author: Yong, Sarah Ee Fang
date: 2020-04-21
url: https://doi.org/10.1016/s1473-3099(20)30273-5
doi: 10.1016/s1473-3099(20)30273-5
abstract:
  BACKGROUND: Elucidation of the chain of disease transmission and identification of the source of coronavirus disease 2019 (COVID-19) infections are crucial for effective disease containment. We describe an epidemiological investigation that, with use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays, established links between three clusters of COVID-19. METHODS: In Singapore, active case-finding and contact tracing were undertaken for all COVID-19 cases. Diagnosis for acute disease was confirmed with RT-PCR testing. When epidemiological information suggested that people might have been nodes of disease transmission but had recovered from illness, SARS-CoV-2 IgG serology testing was used to establish past infection. FINDINGS: Three clusters of COVID-19, comprising 28 locally transmitted cases, were identified in Singapore; these clusters were from two churches (Church A and Church B) and a family gathering. The clusters in Church A and Church B were linked by an individual from Church A (A2), who transmitted SARS-CoV-2 infection to the primary case from Church B (F1) at a family gathering they both attended on Jan 25, 2020. All cases were confirmed by RT-PCR testing because they had active disease, except for A2, who at the time of testing had recovered from their illness and tested negative. This individual was eventually diagnosed with past infection by serological testing. ELISA assays showed an optical density of more than 1·4 for SARS-CoV-2 nucleoprotein and receptor binding domain antigens in titres up to 1/400, and viral neutralisation was noted in titres up to 1/320. INTERPRETATION: Development and application of a serological assay has helped to establish connections between COVID-19 clusters in Singapore. Serological testing can have a crucial role in identifying convalescent cases or people with milder disease who might have been missed by other surveillance methods. FUNDING: National Research Foundation (Singapore), National Natural Science Foundation (China), and National Medical Research Council (Singapore).


id: cord-268074-9mact9br
author: Bi, Qifang
date: 2020-04-27
url: https://www.ncbi.nlm.nih.gov/pubmed/32353347/
doi: 10.1016/s1473-3099(20)30287-5
title:
  Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study

abstract:
  BACKGROUND: Rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, prompted heightened surveillance in Shenzhen, China. The resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control measures. METHODS: From Jan 14 to Feb 12, 2020, the Shenzhen Center for Disease Control and Prevention identified 391 SARS-CoV-2 cases and 1286 close contacts. We compared cases identified through symptomatic surveillance and contact tracing, and estimated the time from symptom onset to confirmation, isolation, and admission to hospital. We estimated metrics of disease transmission and analysed factors influencing transmission risk. FINDINGS: Cases were older than the general population (mean age 45 years) and balanced between males (n=187) and females (n=204). 356 (91%) of 391 cases had mild or moderate clinical severity at initial assessment. As of Feb 22, 2020, three cases had died and 225 had recovered (median time to recovery 21 days; 95% CI 20–22). Cases were isolated on average 4·6 days (95% CI 4·1–5·0) after developing symptoms; contact tracing reduced this by 1·9 days (95% CI 1·1–2·7). Household contacts and those travelling with a case were at higher risk of infection (odds ratio 6·27 [95% CI 1·49–26·33] for household contacts and 7·06 [1·43–34·91] for those travelling with a case) than other close contacts. The household secondary attack rate was 11·2% (95% CI 9·1–13·8), and children were as likely to be infected as adults (infection rate 7·4% in children <10 years vs population average of 6·6%). The observed reproductive number (R) was 0·4 (95% CI 0·3–0·5), with a mean serial interval of 6·3 days (95% CI 5·2–7·6). INTERPRETATION: Our data on cases as well as their infected and uninfected close contacts provide key insights into the epidemiology of SARS-CoV-2. This analysis shows that isolation and contact tracing reduce the time during which cases are infectious in the community, thereby reducing the R. The overall impact of isolation and contact tracing, however, is uncertain and highly dependent on the number of asymptomatic cases. Moreover, children are at a similar risk of infection to the general population, although less likely to have severe symptoms; hence they should be considered in analyses of transmission and control. FUNDING: Emergency Response Program of Harbin Institute of Technology, Emergency Response Program of Peng Cheng Laboratory, US Centers for Disease Control and Prevention.


id: cord-269838-1943g1ha
author: Haffizulla, Jason
date: 2014-05-19
url: https://www.ncbi.nlm.nih.gov/pubmed/24852376/
doi: 10.1016/s1473-3099(14)70717-0
title:
  Effect of nitazoxanide in adults and adolescents with acute uncomplicated influenza: a double-blind, randomised, placebo-controlled, phase 2b/3 trial

abstract:
  BACKGROUND: Influenza is an important cause of morbidity and mortality worldwide. Treatment options are scarce, and new drugs with novel mechanisms of action are needed. We aimed to assess the efficacy and safety of nitazoxanide, a thiazolide anti-infective, for treatment of acute uncomplicated influenza. METHODS: We did a double-blind, randomised, placebo-controlled, phase 2b/3 trial in 74 primary care clinics in the USA between Dec 27, 2010, and April 30, 2011. We enrolled participants aged 12–65 years with fever, at least one respiratory symptom, and one constitutional symptom of influenza within 48 h of symptom onset. We randomly assigned participants to receive either nitazoxanide 600 mg, nitazoxanide 300 mg, or placebo twice daily for 5 days, (ratio 1:1:1) and followed them up for 28 days. Randomisation lists were computer generated and done in blocks of three. Sponsor, investigators, study monitors, patients, and laboratory personnel were all masked to treatment allocation in the study. The primary endpoint was the time from first dose to alleviation of symptoms. The primary analysis was by intention-to-treat for participants with influenza infection confirmed by RT-PCR or culture at baseline. This trial is registered with ClinicalTrials.gov, number NCT01227421. FINDINGS: Of 650 participants screened, 624 (96%) were enrolled. Of these, 212 were randomly assigned to receive placebo twice a day, 201 to receive nitazoxanide 300 mg twice a day, and 211 to receive nitazoxanide 600 mg a day. The median duration of symptoms for participants receiving placebo was 116·7 h (95% CI 108·1–122·1) compared with 95·5 h (84·0–108·0; p=0·0084) for those receiving 600 mg nitazoxanide and 109·1 h (96·1–129·5, p=0·52) for those receiving 300 mg nitazoxanide. Adverse events were similar between the three groups, the most common being headache reported by 24 (11%) of 212 patients enrolled in placebo group, 12 (6%) of 201 patients in the low-dose group, and 17 (8%) of 211 patients in the high-dose group, or diarrhoea, reported by seven (3%) patients in the placebo group, four (2%) patients enrolled in the low-dose group, and 17 (8%) patients in the high-dose group. INTERPRETATION: Treatment with nitazoxanide 600 mg twice daily for 5 days was associated with a reduction of the duration of symptoms in participants with acute uncomplicated influenza. Further studies are warranted to confirm these findings and to assess efficacy of the drug alone or in combination with existing drugs in seriously ill patients and those at risk of influenza complications. FUNDING: Romark Laboratories LC.


id: cord-270602-599vweqe
title: Marine natural products and their potential applications as anti-infective agents
author: Donia, Marwa
date: 2003-05-22
txt: ./txt/cord-270602-599vweqe.txt
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url: https://www.sciencedirect.com/science/article/pii/S1473309903006558
doi: 10.1016/s1473-3099(03)00655-8
summary:
  Although many marine-product clinical trials are for cancer chemotherapy, drug resistance, emerging infectious diseases, and the threat of bioterrorism have all contributed to the interest in assessing natural ocean products in the treatment of infectious organisms. Many marine natural products have successfully advanced to the late stages of clinical trials, including dolastatin 10, ecteinascidin-743, kahalalide F, and aplidine, and a growing number of candidates have been selected as promising leads for extended preclinical assessment. Many marine natural products have successfully advanced to the late stages of clinical trials, including dolastatin 10, ecteinascidin-743, kahalalide F, and aplidine, and a growing number of candidates have been selected as promising leads for extended preclinical assessment. 6 In this review, we focus on the pharmacologically tested marine leads that have shown in-vivo efficacy or potent invitro activity against infectious and parasitic diseases, including malaria, toxoplasmosis, trypanosomiasis, and viral, bacterial, and fungal infections.

abstract:
  The oceans are a unique resource that provide a diverse array of natural products, primarily from invertebrates such as sponges, tunicates, bryozoans, and molluscs, and from marine bacteria and cyanobacteria. As infectious diseases evolve and develop resistance to existing pharmaceuticals, the marine environment provides novel leads against fungal, parasitic, bacterial, and viral diseases. Many marine natural products have successfully advanced to the late stages of clinical trials, including dolastatin 10, ecteinascidin-743, kahalalide F, and aplidine, and a growing number of candidates have been selected as promising leads for extended preclinical assessment. Although many marine-product clinical trials are for cancer chemotherapy, drug resistance, emerging infectious diseases, and the threat of bioterrorism have all contributed to the interest in assessing natural ocean products in the treatment of infectious organisms. In this review, we focus on the pharmacologically tested marine leads that have shown in-vivo efficacy or potent in-vitro activity against infectious and parasitic diseases.


id: cord-272135-a09bf50o
author: Brouqui, Philippe
date: 2009-04-22
url: https://www.ncbi.nlm.nih.gov/pubmed/19393960/
doi: 10.1016/s1473-3099(09)70070-2
title:
  Infection control in the management of highly pathogenic infectious diseases: consensus of the European Network of Infectious Disease

abstract:
  The European Network for Infectious Diseases (EUNID) is a network of clinicians, public health epidemiologists, microbiologists, infection control, and critical-care doctors from the European member states, who are experienced in the management of patients with highly infectious diseases. We aim to develop a consensus recommendation for infection control during clinical management and invasive procedures in such patients. After an extensive literature review, draft recommendations were amended jointly by 27 partners from 15 European countries. Recommendations include repetitive training of staff to ascertain infection control, systematic use of cough and respiratory etiquette at admission to the emergency department, fluid sampling in the isolation room, and analyses in biosafety level 3/4 laboratories, and preference for point-of-care bedside laboratory tests. Children should be cared for by paediatricians and intensive-care patients should be cared for by critical-care doctors in high-level isolation units (HLIU). Invasive procedures should be avoided if unnecessary or done in the HLIU, as should chest radiography, ultrasonography, and renal dialysis. Procedures that require transport of patients out of the HLIU should be done during designated sessions or hours in secure transport. Picture archiving and communication systems should be used. Post-mortem examination should be avoided; biopsy or blood collection is preferred.


id: cord-272274-p3oulo34
author: Teboh-Ewungkem, Miranda I
date: 2020-09-21
url: https://api.elsevier.com/content/article/pii/S1473309920307635
doi: 10.1016/s1473-3099(20)30763-5
abstract: nan
title:
  COVID-19 in malaria-endemic regions: potential consequences for malaria intervention coverage, morbidity, and mortality


id: cord-273910-fna7s9te
title: Innate immunogenetics: a tool for exploring new frontiers of host defence
author: Bochud, Pierre-Yves
date: 2007-07-20
url: https://api.elsevier.com/content/article/pii/S1473309907701858
doi: 10.1016/s1473-3099(07)70185-8
abstract:
  The discovery of innate immune genes, such as those encoding Toll-like receptors (TLRs), nucleotide-binding oligomerisation domain-like receptors (NLRs), and related signal-transducing molecules, has led to a substantial improvement of our understanding of innate immunity. Recent immunogenetic studies have associated polymorphisms of the genes encoding TLRs, NLRs, and key signal-transducing molecules, such as interleukin-1 receptor-associated kinase 4 (IRAK4), with increased susceptibility to, or outcome of, infectious diseases. With the availability of high-throughput genotyping techniques, it is becoming increasingly evident that analyses of genetic polymorphisms of innate immune genes will further improve our knowledge of the host antimicrobial defence response and help in identifying individuals who are at increased risk of life-threatening infections. This is likely to open new perspectives for the development of diagnostic, predictive, and preventive management strategies to combat infectious diseases.


id: cord-277342-40d24mvm
title: SARS-CoV-2: virus dynamics and host response
author: Chen, Yu
date: 2020-03-23
txt: ./txt/cord-277342-40d24mvm.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1473309920302358
doi: 10.1016/s1473-3099(20)30235-8
abstract: nan
summary:
  In The Lancet Infectious Diseases, Kelvin To and colleagues 4 report the viral load and antibody profiles of a cohort of 23 patients admitted to hospital with COVID-19. First, the high viral load during the early phase of illness suggests that patients could be most infectious during this period, and it might account for the high transmissibility of SARS-CoV-2. Second, age was associated with viral load in this study, which could explain the high degree of severe disease in older patients with SARS-CoV-2. 5, 6 The high viral load in elderly patients is associated not only with low immunity but also with high expression of the ACE2 receptor (the cellentry receptor for SARS-CoV-2) in older adults. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore


id: cord-278256-dmrtsxik
author: Qiu, Haiyan
date: 2020-03-25
url: https://api.elsevier.com/content/article/pii/S1473309920301985
doi: 10.1016/s1473-3099(20)30198-5
title:
  Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study

abstract:
  BACKGROUND: Since December, 2019, an outbreak of coronavirus disease 2019 (COVID-19) has spread globally. Little is known about the epidemiological and clinical features of paediatric patients with COVID-19. METHODS: We retrospectively retrieved data for paediatric patients (aged 0–16 years) with confirmed COVID-19 from electronic medical records in three hospitals in Zhejiang, China. We recorded patients' epidemiological and clinical features. FINDINGS: From Jan 17 to March 1, 2020, 36 children (mean age 8·3 [SD 3·5] years) were identified to be infected with severe acute respiratory syndrome coronavirus 2. The route of transmission was by close contact with family members (32 [89%]) or a history of exposure to the epidemic area (12 [33%]); eight (22%) patients had both exposures. 19 (53%) patients had moderate clinical type with pneumonia; 17 (47%) had mild clinical type and either were asymptomatic (ten [28%]) or had acute upper respiratory symptoms (seven [19%]). Common symptoms on admission were fever (13 [36%]) and dry cough (seven [19%]). Of those with fever, four (11%) had a body temperature of 38·5°C or higher, and nine (25%) had a body temperature of 37·5–38·5°C. Typical abnormal laboratory findings were elevated creatine kinase MB (11 [31%]), decreased lymphocytes (11 [31%]), leucopenia (seven [19%]), and elevated procalcitonin (six [17%]). Besides radiographic presentations, variables that were associated significantly with severity of COVID-19 were decreased lymphocytes, elevated body temperature, and high levels of procalcitonin, D-dimer, and creatine kinase MB. All children received interferon alfa by aerosolisation twice a day, 14 (39%) received lopinavir–ritonavir syrup twice a day, and six (17%) needed oxygen inhalation. Mean time in hospital was 14 (SD 3) days. By Feb 28, 2020, all patients were cured. INTERPRETATION: Although all paediatric patients in our cohort had mild or moderate type of COVID-19, the large proportion of asymptomatic children indicates the difficulty in identifying paediatric patients who do not have clear epidemiological information, leading to a dangerous situation in community-acquired infections. FUNDING: Ningbo Clinical Research Center for Children's Health and Diseases, Ningbo Reproductive Medicine Centre, and Key Scientific and Technological Innovation Projects of Wenzhou.


id: cord-279001-l5ogbl5p
title: Can we contain the COVID-19 outbreak with the same measures as for SARS?
author: Wilder-Smith, Annelies
date: 2020-03-05
txt: ./txt/cord-279001-l5ogbl5p.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/32145768/
doi: 10.1016/s1473-3099(20)30129-8
summary:
  COVID-19 differs from SARS in terms of infectious period, transmissibility, clinical severity, and extent of community spread. Even if traditional public health measures are not able to fully contain the outbreak of COVID-19, they will still be effective in reducing peak incidence and global deaths. In November, 2002, the severe acute respiratory syn drome coronavirus (SARSCoV) emerged in China causing global anxiety as the outbreak rapidly spread, and by July, 2003, had resulted in over 8000 cases in 26 countries. In the absence of vaccines and specific treatment, the only available public health tools to control persontoperson transmittable diseases are isolation and quarantine, social distancing, and community containment measures. Isolation, quarantine, social distancing and community containment: pivotal role for oldstyle public health measures in the novel coronavirus (2019nCoV) outbreak Public health measures to control the spread of the severe acute respiratory syndrome during the outbreak in Toronto

abstract:
  The severe acute respiratory syndrome (SARS) outbreak in 2003 resulted in more than 8000 cases and 800 deaths. SARS was eventually contained by means of syndromic surveillance, prompt isolation of patients, strict enforcement of quarantine of all contacts, and in some areas top-down enforcement of community quarantine. By interrupting all human-to-human transmission, SARS was effectively eradicated. By contrast, by Feb 28, 2020, within a matter of 2 months since the beginning of the outbreak of coronavirus disease 2019 (COVID-19), more than 82 000 confirmed cases of COVID-19 have been reported with more than 2800 deaths. Although there are striking similarities between SARS and COVID-19, the differences in the virus characteristics will ultimately determine whether the same measures for SARS will also be successful for COVID-19. COVID-19 differs from SARS in terms of infectious period, transmissibility, clinical severity, and extent of community spread. Even if traditional public health measures are not able to fully contain the outbreak of COVID-19, they will still be effective in reducing peak incidence and global deaths. Exportations to other countries need not result in rapid large-scale outbreaks, if countries have the political will to rapidly implement countermeasures.


id: cord-279557-hk77e3pp
author: Drosten, Christian
date: 2013-06-17
url: https://doi.org/10.1016/s1473-3099(13)70154-3
doi: 10.1016/s1473-3099(13)70154-3
title:
  Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection

abstract:
  BACKGROUND: The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus involved in cases and case clusters of severe acute respiratory infection in the Arabian Peninsula, Tunisia, Morocco, France, Italy, Germany, and the UK. We provide a full description of a fatal case of MERS-CoV infection and associated phylogenetic analyses. METHODS: We report data for a patient who was admitted to the Klinikum Schwabing (Munich, Germany) for severe acute respiratory infection. We did diagnostic RT-PCR and indirect immunofluorescence. From time of diagnosis, respiratory, faecal, and urine samples were obtained for virus quantification. We constructed a maximum likelihood tree of the five available complete MERS-CoV genomes. FINDINGS: A 73-year-old man from Abu Dhabi, United Arab Emirates, was transferred to Klinikum Schwabing on March 19, 2013, on day 11 of illness. He had been diagnosed with multiple myeloma in 2008, and had received several lines of treatment. The patient died on day 18, due to septic shock. MERS-CoV was detected in two samples of bronchoalveolar fluid. Viral loads were highest in samples from the lower respiratory tract (up to 1·2 × 10(6) copies per mL). Maximum virus concentration in urine samples was 2691 RNA copies per mL on day 13; the virus was not present in the urine after renal failure on day 14. Stool samples obtained on days 12 and 16 contained the virus, with up to 1031 RNA copies per g (close to the lowest detection limit of the assay). One of two oronasal swabs obtained on day 16 were positive, but yielded little viral RNA (5370 copies per mL). No virus was detected in blood. The full virus genome was combined with four other available full genome sequences in a maximum likelihood phylogeny, correlating branch lengths with dates of isolation. The time of the common ancestor was halfway through 2011. Addition of novel genome data from an unlinked case treated 6 months previously in Essen, Germany, showed a clustering of viruses derived from Qatar and the United Arab Emirates. INTERPRETATION: We have provided the first complete viral load profile in a case of MERS-CoV infection. MERS-CoV might have shedding patterns that are different from those of severe acute respiratory syndrome and so might need alternative diagnostic approaches. FUNDING: European Union; German Centre for Infection Research; German Research Council; and German Ministry for Education and Research.


id: cord-279765-sb1ifyfx
title: A promising inactivated whole-virion SARS-CoV-2 vaccine
author: Isakova-Sivak, Irina
date: 2020-10-15
txt: ./txt/cord-279765-sb1ifyfx.txt
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url: https://doi.org/10.1016/s1473-3099(20)30832-x
doi: 10.1016/s1473-3099(20)30832-x
abstract: nan
summary:
  In this regard, the study by Shengli Xia and colleagues 7 is timely because it provides valuable evidence for the safety and immunogenicity of a β-propiolactone inactivated aluminium hydroxideadjuvanted whole-virion SARS-CoV-2 vaccine candidate developed by China National Biotec Group and the Beijing Institute of Biological Products (BBIBP-CorV), which was tested in randomised, double-blind, placebocontrolled phase 1/2 clinical trials in healthy individuals aged 18 years and older. Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial Effect of an inactivated vaccine against SARS-CoV-2 on safety and immunogenicity outcomes: interim analysis of 2 randomized clinical trials Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBIBP-CorV: a randomised, double-blind, placebo-controlled, phase 1/2 trial


id: cord-281529-2rec51xg
title: Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation
author: Haagmans, Bart L
date: 2013-12-17
url: https://www.ncbi.nlm.nih.gov/pubmed/24355866/
doi: 10.1016/s1473-3099(13)70690-x
abstract:
  BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe lower respiratory tract infection in people. Previous studies suggested dromedary camels were a reservoir for this virus. We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013. METHODS: We took nose swabs, rectal swabs, and blood samples from all camels on the Qatari farm. We tested swabs with RT-PCR, with amplification targeting the E gene (upE), nucleocapsid (N) gene, and open reading frame (ORF) 1a. PCR positive samples were tested by different MERS-CoV specific PCRs and obtained sequences were used for phylogentic analysis together with sequences from the linked human cases and other human cases. We tested serum samples from the camels for IgG immunofluorescence assay, protein microarray, and virus neutralisation assay. FINDINGS: We obtained samples from 14 camels on Oct 17, 2013. We detected MERS-CoV in nose swabs from three camels by three independent RT-PCRs and sequencing. The nucleotide sequence of an ORF1a fragment (940 nucleotides) and a 4·2 kb concatenated fragment were very similar to the MERS-CoV from two human cases on the same farm and a MERS-CoV isolate from Hafr-Al-Batin. Eight additional camel nose swabs were positive on one or more RT-PCRs, but could not be confirmed by sequencing. All camels had MERS-CoV spike-binding antibodies that correlated well with the presence of neutralising antibodies to MERS-CoV. INTERPRETATION: Our study provides virological confirmation of MERS-CoV in camels and suggests a recent outbreak affecting both human beings and camels. We cannot conclude whether the people on the farm were infected by the camels or vice versa, or if a third source was responsible. FUNDING: European Union projects EMPERIE (contract number 223498), ANTIGONE (contract number 278976), and the VIRGO consortium.


id: cord-282530-55lhjfm8
author: Carsana, Luca
date: 2020-06-08
url: https://www.ncbi.nlm.nih.gov/pubmed/32526193/
doi: 10.1016/s1473-3099(20)30434-5
title:
  Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study

abstract:
  BACKGROUND: COVID-19 is characterised by respiratory symptoms, which deteriorate into respiratory failure in a substantial proportion of cases, requiring intensive care in up to a third of patients admitted to hospital. Analysis of the pathological features in the lung tissues of patients who have died with COVID-19 could help us to understand the disease pathogenesis and clinical outcomes. METHODS: We systematically analysed lung tissue samples from 38 patients who died from COVID-19 in two hospitals in northern Italy between Feb 29 and March 24, 2020. The most representative areas identified at macroscopic examination were selected, and tissue blocks (median seven, range five to nine) were taken from each lung and fixed in 10% buffered formalin for at least 48 h. Tissues were assessed with use of haematoxylin and eosin staining, immunohistochemical staining for inflammatory infiltrate and cellular components (including staining with antibodies against CD68, CD3, CD45, CD61, TTF1, p40, and Ki-67), and electron microscopy to identify virion localisation. FINDINGS: All cases showed features of the exudative and proliferative phases of diffuse alveolar damage, which included capillary congestion (in all cases), necrosis of pneumocytes (in all cases), hyaline membranes (in 33 cases), interstitial and intra-alveolar oedema (in 37 cases), type 2 pneumocyte hyperplasia (in all cases), squamous metaplasia with atypia (in 21 cases), and platelet–fibrin thrombi (in 33 cases). The inflammatory infiltrate, observed in all cases, was largely composed of macrophages in the alveolar lumina (in 24 cases) and lymphocytes in the interstitium (in 31 cases). Electron microscopy revealed that viral particles were predominantly located in the pneumocytes. INTERPRETATION: The predominant pattern of lung lesions in patients with COVID-19 patients is diffuse alveolar damage, as described in patients infected with severe acute respiratory syndrome and Middle East respiratory syndrome coronaviruses. Hyaline membrane formation and pneumocyte atypical hyperplasia are frequent. Importantly, the presence of platelet–fibrin thrombi in small arterial vessels is consistent with coagulopathy, which appears to be common in patients with COVID-19 and should be one of the main targets of therapy. FUNDING: None.


id: cord-288807-sw6teq1n
title: Potential factors linked to high COVID-19 death rates in British minority ethnic groups
author: Cook, Marion
date: 2020-07-17
txt: ./txt/cord-288807-sw6teq1n.txt
cache: ./cache/cord-288807-sw6teq1n.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1473309920305831
doi: 10.1016/s1473-3099(20)30583-1
abstract: nan
summary:
  key: cord-288807-sw6teq1n title: Potential factors linked to high COVID-19 death rates in British minority ethnic groups cord_uid: sw6teq1n 2·3 12·5 0 indicates absent or very low prevalence. NA=not available, although sickle cell trait was found in babies of all ethnic groups in the NHS sickle cell and thalassaemia data report, 2013-14. 5 *Predicted COVID-19 fatalities based on geography and demographics and actual hospital deaths, relative to white British, by ethnic group. Table: COVID-19 fatalities and prevalence of haemolytic disorders and anaemia among UK ethnic groups Mapping the presence of sickle cell and beta-thalassaemia in England: estimating and validating ethnic-specific rates European Association for the Study of the Liver. EASL clinical practice guidelines for HFE hemochromatosis The epidemiology of the haemoglobin level-a study of 1057 subjects in general practice NHS Sickle Cell and Thalassaemia Screening Programme. Data report 2013/14. Are some ethnic groups more vulnerable to COVID-19 than others? London: The Institute for Fiscal Studies


id: cord-288867-iicfe7il
title: COVID-19: when should quarantine be enforced?
author: Bauch, Chris T
date: 2020-05-20
txt: ./txt/cord-288867-iicfe7il.txt
cache: ./cache/cord-288867-iicfe7il.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S147330992030428X
doi: 10.1016/s1473-3099(20)30428-x
abstract: nan
summary:
  These questions are how we might think of some of the dilemmas created by the COVID-19 pandemic, which presents us with difficult trade-offs in equity, economics, public health, and civil liberties. Plainly put, they ask the question: should health authorities place potentially exposed individuals into a quarantine setting where their separation from others can be enforced, or should authorities simply let them go home, ask them to avoid contacts, and monitor them for COVID-19 symptoms through phone calls or health-care visits? Aware of this dilemma, Peak and colleagues 1 use a mathematical model of the early spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections to establish the conditions under which individual quarantine works better than active monitoring. Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study


id: cord-289744-suiqh3gv
author: Lafolie, Jérémy
date: 2018-10-30
url: https://doi.org/10.1016/s1473-3099(18)30479-1
doi: 10.1016/s1473-3099(18)30479-1
title:
  Assessment of blood enterovirus PCR testing in paediatric populations with fever without source, sepsis-like disease, or suspected meningitis: a prospective, multicentre, observational cohort study

abstract:
  BACKGROUND: Enteroviruses are the most frequent cause of acute meningitis and are seen increasingly in sepsis-like disease and fever without source in the paediatric population. Detection of enterovirus in cerebrospinal fluid (CSF) specimens by PCR is the gold standard diagnostic test. Our aim was to assess a method of detecting enterovirus in blood specimens by PCR. METHODS: We did a prospective, multicentre, observational study at 35 French paediatric and emergency departments in 16 hospitals. We recruited newborn babies (aged ≤28 days) and infants (aged >28 days to ≤2 years) with fever without source, sepsis-like disease, or suspected meningitis, and children (aged >2 years to ≤16 years) with suspected meningitis, who were admitted to a participating hospital. We used a standardised form to obtain demographic, clinical, and laboratory data, which were anonymised. Enterovirus PCR testing was done in blood and CSF specimens. FINDINGS: Between June 1, 2015, and Oct 31, 2015, and between June 1, 2016, and Oct 31, 2016, we enrolled 822 patients, of whom 672 had enterovirus PCR testing done in blood and CSF specimens. Enterovirus was detected in 317 (47%) patients in either blood or CSF, or both (71 newborn babies, 83 infants, and 163 children). Detection of enterovirus was more frequent in blood samples than in CSF specimens of newborn babies (70 [99%] of 71 vs 62 [87%] of 71; p=0·011) and infants (76 [92%] of 83 vs 62 [75%] of 83; p=0·008), and was less frequent in blood samples than in CSF specimens of children (90 [55%] of 163 vs 148 [91%] of 163; p<0·0001). Detection of enterovirus was more frequent in blood samples than in CSF specimens of infants aged 2 years or younger with fever without source (55 [100%] of 55 vs 41 [75%] of 55; p=0·0002) or with sepsis-like disease (16 [100%] of 16 vs nine [56%] of 16; p=0·008). Detection of enterovirus was less frequent in blood than in CSF of patients with suspected meningitis (165 [67%] of 246 vs 222 [90%] of 246; p<0·0001). INTERPRETATION: Testing for enterovirus in blood by PCR should be an integral part of clinical practice guidelines for infants aged 2 years or younger. This testing could decrease the length of hospital stay and reduce exposure to antibiotics for low-risk patients admitted to the emergency department with febrile illness. FUNDING: University Hospital Clermont-Ferrand.


id: cord-291821-ovfqfurf
title: Emergence of medicine for mass gatherings: lessons from the Hajj
author: Memish, Ziad A
date: 2011-12-19
url: https://www.sciencedirect.com/science/article/pii/S1473309911703371
doi: 10.1016/s1473-3099(11)70337-1
abstract:
  Although definitions of mass gatherings (MG) vary greatly, they consist of large numbers of people attending an event at a specific site for a finite time. Examples of MGs include World Youth Day, the summer and winter Olympics, rock concerts, and political rallies. Some of the largest MGs are spiritual in nature. Among all MGs, the public health issues, associated with the Hajj (an annual pilgrimage to Mecca, Saudi Arabia) is clearly the best reported—probably because of its international or even intercontinental implications in terms of the spread of infectious disease. Hajj routinely attracts 2·5 million Muslims for worship. WHO's global health initiatives have converged with Saudi Arabia's efforts to ensure the wellbeing of pilgrims, contain infectious diseases, and reinforce global health security through the management of the Hajj. Both initiatives emphasise the importance of MG health policies guided by sound evidence and based on experience and the timeliness of calls for a new academic science-based specialty of MG medicine.


id: cord-293540-45awgabp
title: Point-of-care testing for community-acquired pneumonia
author: Drancourt, Michel
date: 2013-07-23
txt: ./txt/cord-293540-45awgabp.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1473309913701658
doi: 10.1016/s1473-3099(13)70165-8
abstract: nan
summary:
  The rate and timing of pandemic A H1N1 virus infections might have revealed the diff erences in H7N9 disease outcome, by contrast with historical infections with seasonal infl uenza A H3N2 viruses. To avoid this delay, we introduced point-of-care (POC) microbiology laboratories near emergency departments where patients with community-acquired pneumonia are seen fi rst. However, it should be noted that not all pathogens that can cause community-acquired pneumonia can be detected by POC tests, and molecular tests for Staphylococus aureus have not been approved by the US Food and Drug Administration (FDA) or the European Conformity (CE). 9 This new capacity of POC tests increases the number of diagnoses 11 and underscores that community-acquired pneumonia can result from co-infection with several pathogens, 10 which will challenge common notions about causation and management. Furthermore, detection by POC testing of an abnormal increase in group A streptococci might suggest co-infection with infl uenza.


id: cord-296573-4c9gch5b
author: To, Kelvin KW
date: 2013-08-19
url: https://www.sciencedirect.com/science/article/pii/S1473309913701671
doi: 10.1016/s1473-3099(13)70167-1
title:
  The emergence of influenza A H7N9 in human beings 16 years after influenza A H5N1: a tale of two cities

abstract:
  Infection with either influenza A H5N1 virus in 1997 or avian influenza A H7N9 virus in 2013 caused severe pneumonia that did not respond to typical or atypical antimicrobial treatment, and resulted in high mortality. Both viruses are reassortants with internal genes derived from avian influenza A H9N2 viruses that circulate in Asian poultry. Both viruses have genetic markers of mammalian adaptation in their haemagglutinin and polymerase PB2 subunits, which enhanced binding to human-type receptors and improved replication in mammals, respectively. Hong Kong (affected by H5N1 in 1997) and Shanghai (affected by H7N9 in 2013) are two rapidly flourishing cosmopolitan megacities that were increasing in human population and poultry consumption before the outbreaks. Both cities are located along the avian migratory route at the Pearl River delta and Yangtze River delta. Whether the widespread use of the H5N1 vaccine in east Asia—with suboptimum biosecurity measures in live poultry markets and farms—predisposed to the emergence of H7N9 or other virus subtypes needs further investigation. Why H7N9 seems to be more readily transmitted from poultry to people than H5N1 is still unclear.


id: cord-303272-1w8epdht
author: Reusken, Chantal BEM
date: 2013-08-09
url: https://api.elsevier.com/content/article/pii/S1473309913701646
doi: 10.1016/s1473-3099(13)70164-6
title:
  Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study

abstract:
  BACKGROUND: A new betacoronavirus—Middle East respiratory syndrome coronavirus (MERS-CoV)—has been identified in patients with severe acute respiratory infection. Although related viruses infect bats, molecular clock analyses have been unable to identify direct ancestors of MERS-CoV. Anecdotal exposure histories suggest that patients had been in contact with dromedary camels or goats. We investigated possible animal reservoirs of MERS-CoV by assessing specific serum antibodies in livestock. METHODS: We took sera from animals in the Middle East (Oman) and from elsewhere (Spain, Netherlands, Chile). Cattle (n=80), sheep (n=40), goats (n=40), dromedary camels (n=155), and various other camelid species (n=34) were tested for specific serum IgG by protein microarray using the receptor-binding S1 subunits of spike proteins of MERS-CoV, severe acute respiratory syndrome coronavirus, and human coronavirus OC43. Results were confirmed by virus neutralisation tests for MERS-CoV and bovine coronavirus. FINDINGS: 50 of 50 (100%) sera from Omani camels and 15 of 105 (14%) from Spanish camels had protein-specific antibodies against MERS-CoV spike. Sera from European sheep, goats, cattle, and other camelids had no such antibodies. MERS-CoV neutralising antibody titres varied between 1/320 and 1/2560 for the Omani camel sera and between 1/20 and 1/320 for the Spanish camel sera. There was no evidence for cross-neutralisation by bovine coronavirus antibodies. INTERPRETATION: MERS-CoV or a related virus has infected camel populations. Both titres and seroprevalences in sera from different locations in Oman suggest widespread infection. FUNDING: European Union, European Centre For Disease Prevention and Control, Deutsche Forschungsgemeinschaft.


id: cord-313615-cts45n3j
title: Research agenda for mass gatherings: a call to action
author: Tam, John S
date: 2012-01-15
url: https://www.sciencedirect.com/science/article/pii/S147330991170353X
doi: 10.1016/s1473-3099(11)70353-x
abstract:
  Public health research is essential for the development of effective policies and planning to address health security and risks associated with mass gatherings (MGs). Crucial research topics related to MGs and their effects on global health security are discussed in this review. The research agenda for MGs consists of a framework of five major public health research directions that address issues related to reducing the risk of public health emergencies during MGs; restricting the occurrence of non-communicable and communicable diseases; minimisation of the effect of public health events associated with MGs; optimisation of the medical services and treatment of diseases during MGs; and development and application of modern public health measures. Implementation of the proposed research topics would be expected to provide benefits over the medium to long term in planning for MGs.


id: cord-314734-ai0hz4uq
author: Hung, Ivan Fan-Ngai
date: 2020-06-12
url: https://doi.org/10.1016/s1473-3099(20)30364-9
doi: 10.1016/s1473-3099(20)30364-9
title:
  SARS-CoV-2 shedding and seroconversion among passengers quarantined after disembarking a cruise ship: a case series

abstract:
  BACKGROUND: A cruise ship is a closed-off environment that simulates the basic functioning of a city in terms of living conditions and interpersonal interactions. Thus, the Diamond Princess cruise ship, which was quarantined because of an onboard outbreak of COVID-19 in February, 2020, provides an opportunity to define the shedding pattern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patient antibody responses before and after the onset of symptoms. METHODS: We recruited adult (≥18 years) passengers from Hong Kong who had been on board the Diamond Princess cruise ship docked in Yokohama, Japan in February, 2020. All participants had been found to be negative for SARS-CoV-2 by RT-PCR 4 days before disembarking and were transferred to further quarantine in a public estate in Hong Kong, where they were recruited. Participants were prospectively screened by quantitative RT-PCR (RT-qPCR) of nasopharyngeal and throat swabs, and serum IgG and IgM against internal nucleoprotein and the surface spike receptor-binding protein (RBD) of SARS-CoV-2 at baseline (upon entering quarantine) and on days 4, 8, and 12 of quarantine. FINDINGS: On Feb 22, 2020, 215 adults were recruited, of whom nine (4%; 95% CI 2–8) were positive for SARS-CoV-2 by RT-qPCR or serology and were hospitalised. Of these nine patients, nasopharyngeal swab RT-qPCR was positive in eight patients (89%; 57–99) at baseline. All nine patients were positive for anti-RBD IgG by day 8. Eight (89%; 57–99) were simultaneously positive for nasopharyngeal swab RT-PCR and anti-RBD IgG. One patient who was positive for anti-RBD IgG and had a negative viral load had multifocal peripheral ground-glass changes on high-resolution CT that were typical of COVID-19. Five patients (56%; 27–81) with ground-glass changes on high-resolution CT were found to have higher anti-nucleoprotein-IgG OD values on day 8 and 12 and anti-RBD IgG OD value on day 12 than patients without ground-glass changes. Six (67%; 35–88) patients remained asymptomatic throughout the 14-day quarantine period. INTERPRETATION: Patients with COVID-19 can develop asymptomatic lung infection with viral shedding and those with evidence of pneumonia on imaging tend to have an increased antibody response. Positive IgG or IgM confirmed infection of COVID-19 in both symptomatic and asymptomatic patients. A combination of RT-PCR and serology should be implemented for case finding and contact tracing to facilitate early diagnosis, prompt isolation, and treatment. FUNDING: Shaw Foundation Hong Kong; Sanming-Project of Medicine (Shenzhen); High Level-Hospital Program (Guangdong Health Commission).


id: cord-316201-08pyx98r
author: Grout, Andrea
date: 2017-02-01
url: https://doi.org/10.1016/s1473-3099(16)30476-5
doi: 10.1016/s1473-3099(16)30476-5
title:
  Guidelines, law, and governance: disconnects in the global control of airline-associated infectious diseases

abstract:
  International air travel is increasingly affecting the epidemiology of infectious diseases. A particular public health, economic, and political concern is the role of air travel in bringing infectious passengers or vectors to previously non-endemic areas. Yet, little research has been done to investigate either the infection risks associated with air travel or the empirical evidence for the effectiveness of infection control measures on aircraft and at borders. We briefly review the interface between international and national legislation, policy, and guidelines in the context of existing infection risks and possible scenarios. We have found that public health guidance and legislation, which airlines are required to follow, are often contradictory and confusing. Infection control measures for air travel need to be underpinned by coherent and enforceable national and international legislation that is based on solid epidemiological evidence. We recommend further research investment into more effective on-board vector control, health screening, and risk communications strategies, and the development of enforceable and harmonised international legislation.


id: cord-317795-689at1qx
title: Monitoring approaches for health-care workers during the COVID-19 pandemic
author: Bielicki, Julia A
date: 2020-07-23
url: https://www.ncbi.nlm.nih.gov/pubmed/32711692/
doi: 10.1016/s1473-3099(20)30458-8
abstract:
  Health-care workers are crucial to any health-care system. During the ongoing COVID-19 pandemic, health-care workers are at a substantially increased risk of becoming infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and could come to considerable harm as a result. Depending on the phase of the pandemic, patients with COVID-19 might not be the main source of SARS-CoV-2 infection and health-care workers could be exposed to atypical patients, infected family members, contacts, and colleagues, or live in communities of active transmission. Clear strategies to support and appropriately manage exposed and infected health-care workers are essential to ensure effective staff management and to engender trust in the workplace. These management strategies should focus on risk stratification, suitable clinical monitoring, low-threshold access to diagnostics, and decision making about removal from and return to work. Policy makers need to support health-care facilities in interpreting guidance during a pandemic that will probably be characterised by fluctuating local incidence of SARS-CoV-2 to mitigate the impact of this pandemic on their workforce.


id: cord-318683-1yxurnev
title: Confronting the threat of bioterrorism: realities, challenges, and defensive strategies
author: Green, Manfred S
date: 2018-10-16
url: https://www.ncbi.nlm.nih.gov/pubmed/30340981/
doi: 10.1016/s1473-3099(18)30298-6
abstract:
  Global terrorism is a rapidly growing threat to world security, and increases the risk of bioterrorism. In this Review, we discuss the potential threat of bioterrorism, agents that could be exploited, and recent developments in technologies and policy for detecting and controlling epidemics that have been initiated intentionally. The local and international response to infectious disease epidemics, such as the severe acute respiratory syndrome and west African Ebola virus epidemic, revealed serious shortcomings which bioterrorists might exploit when intentionally initiating an epidemic. Development of new vaccines and antimicrobial therapies remains a priority, including the need to expedite clinical trials using new methodologies. Better means to protect health-care workers operating in dangerous environments are also needed, particularly in areas with poor infrastructure. New and improved approaches should be developed for surveillance, early detection, response, effective isolation of patients, control of the movement of potentially infected people, and risk communication. Access to dangerous pathogens should be appropriately regulated, without reducing progress in the development of countermeasures. We conclude that preparedness for intentional outbreaks has the important added value of strengthening preparedness for natural epidemics, and vice versa.


id: cord-320548-oigyut2k
author: Zumla, Alimuddin
date: 2014-09-01
url: https://www.sciencedirect.com/science/article/pii/S147330991470828X
doi: 10.1016/s1473-3099(14)70828-x
title:
  Emerging novel and antimicrobial-resistant respiratory tract infections: new drug development and therapeutic options

abstract:
  The emergence and spread of antimicrobial-resistant bacterial, viral, and fungal pathogens for which diminishing treatment options are available is of major global concern. New viral respiratory tract infections with epidemic potential, such as severe acute respiratory syndrome, swine-origin influenza A H1N1, and Middle East respiratory syndrome coronavirus infection, require development of new antiviral agents. The substantial rise in the global numbers of patients with respiratory tract infections caused by pan-antibiotic-resistant Gram-positive and Gram-negative bacteria, multidrug-resistant Mycobacterium tuberculosis, and multiazole-resistant fungi has focused attention on investments into development of new drugs and treatment regimens. Successful treatment outcomes for patients with respiratory tract infections across all health-care settings will necessitate rapid, precise diagnosis and more effective and pathogen-specific therapies. This Series paper describes the development and use of new antimicrobial agents and immune-based and host-directed therapies for a range of conventional and emerging viral, bacterial, and fungal causes of respiratory tract infections.


id: cord-320970-ru2iw0py
title: Serology testing in the COVID-19 pandemic response
author: Peeling, Rosanna W
date: 2020-07-17
url: https://www.sciencedirect.com/science/article/pii/S147330992030517X
doi: 10.1016/s1473-3099(20)30517-x
abstract:
  The collapse of global cooperation and a failure of international solidarity have led to many low-income and middle-income countries being denied access to molecular diagnostics in the COVID-19 pandemic response. Yet the scarcity of knowledge on the dynamics of the immune response to infection has led to hesitation on recommending the use of rapid immunodiagnostic tests, even though rapid serology tests are commercially available and scalable. On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. The WHO R&D Blue Print expert group identified eight priorities for research and development, of which the highest is to mobilise research on rapid point-of-care diagnostics for use at the community level. This research should inform control programmes of the required performance and utility of rapid serology tests, which, when applied specifically for appropriate public health measures to then be put in place, can make a huge difference.


id: cord-321949-s1qu3odd
title: Rotavirus infection in adults
author: Anderson, Evan J
date: 2004-01-28
url: https://api.elsevier.com/content/article/pii/S1473309904009284
doi: 10.1016/s1473-3099(04)00928-4
abstract:
  Rotavirus has been recognised for 30 years as the most common cause of infectious gastroenteritis in infants and young children. By contrast, the role of rotavirus as a pathogen in adults has long been underappreciated. Spread by faecal-oral transmission, rotavirus infection in adults typically manifests with nausea, malaise, headache, abdominal cramping, diarrhoea, and fever. Infection can also be symptomless. Rotavirus infection in immuno-compromised adults can have a variable course from symptomless to severe and sustained infection. Common epidemiological settings for rotavirus infection among adults include endemic disease, epidemic outbreak, travel-related infection, and disease resulting from child-to-adult transmission. Limited diagnostic and therapeutic alternatives are available for adults with suspected rotavirus infection. Because symptoms are generally self-limiting, supportive care is the rule. Clinicians caring for adults with gastroenteritis should consider rotavirus in the differential diagnosis. In this review we intend to familiarise clinicians who primarily provide care for adult patients with the salient features of rotavirus pathophysiology, clinical presentation, epidemiology, treatment, and prevention.


id: cord-331244-zaguyxm5
title: Confronting the avian influenza threat: vaccine development for a potential pandemic
author: Stephenson, Iain
date: 2004-07-30
url: https://api.elsevier.com/content/article/pii/S1473309904011053
doi: 10.1016/s1473-3099(04)01105-3
abstract:
  Sporadic human infection with avian influenza viruses has raised concern that reassortment between human and avian subtypes could generate viruses of pandemic potential. Vaccination is the principal means to combat the impact of influenza. During an influenza pandemic the immune status of the population would differ from that which exists during interpandemic periods. An emerging pandemic virus will create a surge in worldwide vaccine demand and new approaches in immunisation strategies may be needed to ensure optimum protection of unprimed individuals when vaccine antigen may be limited. The manufacture of vaccines from pathogenic avian influenza viruses by traditional methods is not feasible for safety reasons as well as technical issues. Strategies adopted to overcome these issues include the use of reverse genetic systems to generate reassortant strains, the use of baculovirusexpressed haemagglutinin or related non-pathogenic avian influenza strains, and the use of adjuvants to enhance immunogenicity. In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. Adjuvanted or whole-virus preparations may improve immunogenicity and allow sparing of antigen.


id: cord-332237-8oykgp0h
author: Omrani, Ali S
date: 2014-09-29
url: https://www.sciencedirect.com/science/article/pii/S147330991470920X
doi: 10.1016/s1473-3099(14)70920-x
title:
  Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study

abstract:
  BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) infection is associated with high mortality and has no approved antiviral therapy. We aimed to compare ribavirin and interferon alfa-2a treatment for patients with severe MERS-CoV infection with a supportive therapy only. METHODS: In this retrospective cohort study, we included adults (aged ≥16 years) with laboratory-confirmed MERS-CoV infection and pneumonia needing ventilation support, diagnosed between Oct 23, 2012, and May 1, 2014, at the Prince Sultan Military Medical City (Riyadh, Saudi Arabia). All patients received appropriate supportive care and regular clinical and laboratory monitoring, but patients diagnosed after Sept 16, 2013, were also given oral ribavirin (dose based on calculated creatinine clearance, for 8–10 days) and subcutaneous pegylated interferon alfa-2a (180 μg per week for 2 weeks). The primary endpoint was 14-day and 28-day survival from the date of MERS-CoV infection diagnosis. We used χ(2) and Fischer's exact test to analyse categorical variables and the t test to analyse continuous variables. FINDINGS: We analysed 20 patients who received ribavirin and interferon (treatment group; initiated a median of 3 days [range 0–8] after diagnosis) and 24 who did not (comparator group). Baseline clinical and laboratory characteristics were similar between groups, apart from baseline absolute neutrophil count, which was significantly lower in the comparator group (5·88 × 10(9)/L [SD 3·95] vs 9·88 × 10(9)/L [6·63]; p=0·023). 14 (70%) of 20 patients in the treatment group had survived after 14 days, compared with seven (29%) of 24 in the comparator group (p=0·004). After 28 days, six (30%) of 20 and four (17%) of 24, respectively, had survived (p=0·054). Adverse effects were similar between groups, apart from reduction in haemoglobin, which was significantly greater in the treatment group than in the comparator group (4·32 g/L [SD 2·47] vs 2·14 g/L [1·90]; p=0·002). INTERPRETATION: In patients with severe MERS-CoV infection, ribavirin and interferon alfa-2a therapy is associated with significantly improved survival at 14 days, but not at 28 days. Further assessment in appropriately designed randomised trials is recommended. FUNDING: None.


id: cord-332238-qw2ual51
title: COVID-19 and the coming epidemic in US immigration detention centres
author: Meyer, Jaimie P
date: 2020-04-15
txt: ./txt/cord-332238-qw2ual51.txt
cache: ./cache/cord-332238-qw2ual51.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32304631/
doi: 10.1016/s1473-3099(20)30295-4
abstract: nan
summary:
  Individuals in US Immigration and Customs Enforcement (ICE) detention are at risk from serious consequences resulting from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and inadequate access to appropriate medical care. In the USA, a rapid increase in SARS-CoV-2 infections in every state of the country has resulted in a growing number of hospitalisations, admissions to intensive care units, and deaths in specific age groups and in many people with underlying medical conditions. 1 Individuals who are incarcerated, including immigrants in ICE detention, are among the most vulnerable to infection and complicated disease because of existing drivers of inequality. Immigrants in ICE detention around the country have expressed panic over conditions that put them at exceptionally high risk of an outbreak of COVID-19 and proposed an immediate humanitarian response to mitigate the risk of infection. These actions should include the immediate release on humanitarian parole of individuals at risk of severe disease and death due to COVID-19 infection.


id: cord-354881-7o20cn1x
title: The scientific and ethical feasibility of immunity passports
author: Brown, Rebecca C H
date: 2020-10-16
url: https://api.elsevier.com/content/article/pii/S1473309920307660
doi: 10.1016/s1473-3099(20)30766-0
abstract:
  There is much debate about the use of immunity passports in the response to the COVID-19 pandemic. Some have argued that immunity passports are unethical and impractical, pointing to uncertainties relating to COVID-19 immunity, issues with testing, perverse incentives, doubtful economic benefits, privacy concerns, and the risk of discriminatory effects. We first review the scientific feasibility of immunity passports. Considerable hurdles remain, but increasing understanding of the neutralising antibody response to COVID-19 might make identifying members of the community at low risk of contracting and transmitting COVID-19 possible. We respond to the ethical arguments against immunity passports and give the positive ethical arguments. First, a strong presumption should be in favour of preserving people's free movement if at all feasible. Second, failing to recognise the reduced infection threat immune individuals pose risks punishing people for low-risk behaviour. Finally, further individual and social benefits are likely to accrue from allowing people to engage in free movement. Challenges relating to the implementation of immunity passports ought to be met with targeted solutions so as to maximise their benefit.


