Recent #advances in the #detection of #respiratory virus #infection in #humans (J Med Virol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

J Med Virol. 2020 Jan 15. doi: 10.1002/jmv.25674. [Epub ahead of print]

Recent advances in the detection of respiratory virus infection in humans.

Zhang N1, Wang L2, Deng X3, Liang R3, Su M3, He C3, Hu L3, Su Y3, Ren J3, Yu F3, Du L4, Jiang S4,5.

Author information: 1 Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China. 2 State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China. 3 State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China. 4 Lindsley F. Kimball Research Institute, New York Blood Center, New York, USA. 5 Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.



Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019-nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people’s lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus (RSV), coronavirus, human adenovirus (hAdV), and human rhinovirus (hRV). Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.

This article is protected by copyright. All rights reserved.

KEYWORDS: Respiratory viral infection; adenovirus; coronavirus; diagnostic methods; influenza virus; respiratory syncytial virus; rhinovirus

PMID: 31944312 DOI: 10.1002/jmv.25674

Keywords: Infectious Diseases; Diagnostic tests; 2019-nCoV.


An observational prospective cohort study of the #epidemiology of hospitalized patients with acute #febrile #illness in #Indonesia (PLOS Negl Trop Dis., abstract)

[Source: PLOS Neglected Tropical Diseases, full page: (LINK). Abstract, edited.]


An observational prospective cohort study of the epidemiology of hospitalized patients with acute febrile illness in Indonesia

Muhammad Hussein Gasem , Herman Kosasih , Emiliana Tjitra, Bachti Alisjahbana, Muhammad Karyana, Dewi Lokida, Aaron Neal, Jason Liang, Abu Tholib Aman, Mansyur Arif, Pratiwi Sudarmono, Suharto, Tuti Parwati Merati,  [ … ], for INA-RESPOND


Published: January 10, 2020 / DOI: / This is an uncorrected proof.




The epidemiology of acute febrile illness, a common cause of hospitalization in Indonesia, has not been systematically studied.

Methodology/Principal gindings

This prospective observational study enrolled febrile patients (temperature ≥38°C) aged ≥1 year from July 2013 until June 2016 at eight government referral teaching hospitals in seven provincial capitals in Indonesia. Patients were managed according to the hospital standard-of-care (SOC), and blood samples were drawn for molecular and serological assays. Clinical data, laboratory results, and specimens for additional tests were collected at enrollment, days 14–28, and at three months. Regular follow-up visits were then scheduled for every three months either until symptoms resolved or until one year. In total, this study included 1,486 adult and pediatric patients presenting with multi-organ (768, 51.7%), gastrointestinal (497, 33.0%), respiratory (114, 7.7%), constitutional (62, 4.2%), skin and soft-tissue (24, 1.6%), central nervous system (17, 1.1%), or genitourinary (4, 0.3%) manifestations. Microbiological diagnoses were found in 1,003/1,486 (67.5%) participants, of which 351/1,003 (35.0%) were not diagnosed during hospitalization using SOC diagnostic tests. Missed diagnoses included all cases caused by Rickettsia spp., chikungunya, influenza, and Seoul virus. The most common etiologic agents identified were dengue virus (467, 46.6%), Salmonella spp. (103, 10.3%), and Rickettsia spp. (103, 10.3%). The overall mortality was 89 (5.9%).


Febrile illness in Indonesia has various microbiologic etiologies and substantial overall mortality. Diagnostic limitations and lack of epidemiologic data resulted in potentially treatable, and at times fatal, diseases being missed.


Author summary

In tropical countries like Indonesia, fever due to infectious disease is the most common reason for hospitalization. However, diagnoses are mostly unconfirmed, as diagnostic tests are not available or are not performed due to budget constraints. Consequently, many patients are only treated based on clinical syndromes. To gain a better understanding of the epidemiology of acute fever in Indonesia, we conducted a study at eight hospitals in the seven largest cities from 2013–2016. We enrolled 1,486 subjects aged ≥1 year with acute fever ≥38°C. Blood cultures were mandatory for all subjects, while cultures of other biological specimens, microscopic examinations, and rapid tests for specific pathogens were based on clinical judgment and availability. Retrospectively, we performed molecular and serological testing for a panel of bacterial and viral pathogens for systemic, respiratory, and diarrheal diseases. We found six pathogens to be the most prevalent: dengue virus (47%), Salmonella Typhi/Paratyphi (10%), Rickettsia typhi (10%), influenza virus (7%), Leptospira spp. (5%), and chikungunya virus (4%). Rickettsia typhi, influenza, and chikungunya had not been considered in the differential diagnosis of any subject at the hospitals. Thus, multiple pathogens were associated with acute febrile illnesses, and a subset of treatable cases were missed. This may have resulted in increased overall mortality.


Citation: Gasem MH, Kosasih H, Tjitra E, Alisjahbana B, Karyana M, Lokida D, et al. (2020) An observational prospective cohort study of the epidemiology of hospitalized patients with acute febrile illness in Indonesia. PLoS Negl Trop Dis 14(1): e0007927.

Editor: Florian Marks, International Vaccine Institute, REPUBLIC OF KOREA

Received: December 5, 2018; Accepted: November 14, 2019; Published: January 10, 2020

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, under contract Nos. HHSN261200800001E and HHSN261201500003I. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Infectious Diseases; Indonesia.


#Global #warming threatens #human #thermoregulation and #survival (J Clin Invest., summary)

[Source: Journal of Clinical Investigation, full page: (LINK). Summary, edited.]

Global warming threatens human thermoregulation and survival

Rexford S. Ahima

First published January 6, 2020


There is overwhelming evidence showing that human activities have contributed to global warming over the past century. Global warming has a severe impact on food and water supplies, housing and other infrastructure, health, and economic activities. The human body has thermoregulatory mechanisms that adapt to ambient temperature and maintain normal core body temperature for physiological functions. This JCI Viewpoint article discusses how extreme temperatures driven by global warming disrupt normal thermoregulation and imperil human health and survival.


Keywords: Climate change; Global Warming; Infectious diseases.


#Climatechange brings the #specter of new #infectious diseases (J Clin Invest., summary)

[Source: Journal of Clinical Investigation, full page: (LINK). Summary, edited.]

Climate change brings the specter of new infectious diseases

Arturo Casadevall

First published January 6, 2020


Climate change will bring major changes to the epidemiology of infectious diseases through changes in microbial and vector geographic range. Human defenses against microbial diseases rely on advanced immunity that includes innate and adaptive arms and endothermy, which creates a thermal restriction zone for many microbes. Given that microbes can adapt to higher temperatures, there is concern that global warming will select for microbes with higher heat tolerance that can defeat our endothermy defenses and bring new infectious disease.


Keywords: Climate Change; Global Warming; Infectious Diseases.


Uncrewed #aircraft #systems versus #motorcycles to deliver laboratory #samples in west #Africa: a comparative economic study (Lancet Glob Health, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Lancet Glob Health. 2020 Jan;8(1):e143-e151. doi: 10.1016/S2214-109X(19)30464-4.

Uncrewed aircraft systems versus motorcycles to deliver laboratory samples in west Africa: a comparative economic study.

Ochieng WO1, Ye T2, Scheel C2, Lor A2, Saindon J3, Yee SL2, Meltzer MI4, Kapil V2, Karem K2.

Author information: 1 Karna LLC, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA. Electronic address: 2 Office of the Director, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA. 3 Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA. 4 Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.




Transportation of laboratory samples in low-income and middle-income countries is often constrained by poor road conditions, difficult geographical terrain, and insecurity. These constraints can lead to long turnaround times for laboratory diagnostic tests and hamper epidemic control or patient treatment efforts. Although uncrewed aircraft systems (UAS)-ie, drones-can mitigate some of these transportation constraints, their cost-effectiveness compared with land-based transportation systems is unclear.


We did a comparative economic study of the costs and cost-effectiveness of UAS versus motorcycles in Liberia (west Africa) for transportation of laboratory samples under simulated routine conditions and public health emergency conditions (based on the 2013-16 west African Ebola virus disease epidemic). We modelled three UAS with operational ranges of 30 km, 65 km, and 100 km (UAS30, UAS65, and UAS100) and lifespans of 1000 to 10 000 h, and compared the costs and number of samples transported with an established motorcycle transportation programme (most commonly used by the Liberian Ministry of Health and the charity Riders for Health). Data for UAS were obtained from Skyfire (a UAS consultancy), Vayu (a UAS manufacturer), and Sandia National Laboratories (a private company with UAS research experience). Motorcycle operational data were obtained from Riders for Health. In our model, we included costs for personnel, equipment, maintenance, and training, and did univariate and probabilistic sensitivity analyses for UAS lifespans, range, and accident or failures.


Under the routine scenario, the per sample transport costs were US$0·65 (95% CI 0·01-2·85) and $0·82 (0·56-5·05) for motorcycles and UAS65, respectively. Per-sample transport costs under the emergency scenario were $24·06 (95% CI 21·14-28·20) for motorcycles, $27·42 (95% CI 19·25-136·75) for an unadjusted UAS model with insufficient geographical coverage, and $34·09 (95% CI 26·70-127·40) for an adjusted UAS model with complementary motorcycles. Motorcycles were more cost-effective than short-range UAS (ie, UAS30). However, with increasing range and operational lifespans, UAS became increasingly more cost-effective.


Given the current level of technology, purchase prices, equipment lifespans, and operational flying ranges, UAS are not a viable option for routine transport of laboratory samples in west Africa. Field studies are required to generate evidence about UAS lifespan, failure rates, and performance under different weather conditions and payloads.



Copyright © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.

PMID: 31839129 DOI: 10.1016/S2214-109X(19)30464-4

Keywords: West Africa; Infectious diseases; Society.


#Patterns, #Drivers, and #Challenges of #Vector-Borne #Disease Emergence (Vector Borne Zoo Dis., abstract)

[Source: Vector Borne and Zoonotic Diseases, full page: (LINK). Abstract, edited.]

Patterns, Drivers, and Challenges of Vector-Borne Disease Emergence

Andrea Swei, Lisa I. Couper, Lark L. Coffey, Durrell Kapan, and Shannon Bennett

Published Online: 3 Dec 2019 / DOI:



Vector-borne diseases are emerging at an increasing rate and comprise a disproportionate share of all emerging infectious diseases. Yet, the key ecological and evolutionary dimensions of vector-borne disease that facilitate their emergence have not been thoroughly explored. This study reviews and synthesizes the existing literature to explore global patterns of emerging vector-borne zoonotic diseases (VBZDs) under changing global conditions. We find that the vast majority of emerging VBZDs are transmitted by ticks (Ixodidae) and mosquitoes (Culicidae) and the pathogens transmitted are dominated by Rickettsiaceae bacteria and RNA viruses (Flaviviridae, Bunyaviridae, and Togaviridae). The most common potential driver of these emerging zoonoses is land use change, but for many diseases, the driver is unknown, revealing a critical research gap. While most reported VBZDs are emerging in the northern latitudes, after correcting for sampling bias, Africa is clearly a region with the greatest share of emerging VBZD. We highlight critical gaps in our understanding of VBZD emergence and emphasize the importance of interdisciplinary research and consideration of deeper evolutionary processes to improve our capacity for anticipating where and how such diseases have and will continue to emerge.

Keywords: Infectious Diseases; Mosquitoes; Emerging Diseases.


Developing #vaccines against #epidemic-prone emerging #infectious diseases (Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2019 Nov 27. doi: 10.1007/s00103-019-03061-2. [Epub ahead of print]

Developing vaccines against epidemic-prone emerging infectious diseases.

Bernasconi V1, Kristiansen PA1, Whelan M2, Román RG1, Bettis A1, Yimer SA1, Gurry C1, Andersen SR1, Yeskey D3, Mandi H1, Kumar A1, Holst J1, Clark C1, Cramer JP2, Røttingen JA1,4, Hattchet R1, Saville M2, Norheim G5.

Author information: 1 Coalition for Epidemic Preparedness Innovation (CEPI), Marcus Thranes Gate 2, 0473, Oslo, Norway. 2 Coalition for Epidemic Preparedness Innovation (CEPI), NW1 2BE, London, UK. 3 Coalition for Epidemic Preparedness Innovation (CEPI), Washington, DC, USA. 4 Research Council of Norway, Lysaker, Norway. 5 Coalition for Epidemic Preparedness Innovation (CEPI), Marcus Thranes Gate 2, 0473, Oslo, Norway.



Today’s world is characterized by increasing population density, human mobility, urbanization, and climate and ecological change. This global dynamic has various effects, including the increased appearance of emerging infectious diseases (EIDs), which pose a growing threat to global health security.Outbreaks of EIDs, like the 2013-2016 Ebola outbreak in West Africa or the current Ebola outbreak in Democratic Republic of the Congo (DRC), have not only put populations in low- and middle-income countries (LMIC) at risk in terms of morbidity and mortality, but they also have had a significant impact on economic growth in affected regions and beyond.The Coalition for Epidemic Preparedness Innovation (CEPI) is an innovative global partnership between public, private, philanthropic, and civil society organizations that was launched as the result of a consensus that a coordinated, international, and intergovernmental plan was needed to develop and deploy new vaccines to prevent future epidemics. CEPI is focusing on supporting candidate vaccines against the World Health Organization (WHO) Blueprint priority pathogens MERS-CoV, Nipah virus, Lassa fever virus, and Rift Valley fever virus, as well as Chikungunya virus, which is on the WHO watch list. The current vaccine portfolio contains a wide variety of technologies, ranging across recombinant viral vectors, nucleic acids, and recombinant proteins. To support and accelerate vaccine development, CEPI will also support science projects related to the development of biological standards and assays, animal models, epidemiological studies, and diagnostics, as well as build capacities for future clinical trials in risk-prone contexts.

KEYWORDS: CEPI; Chikungunya; MERS-CoV; Nipah; Rift Valley fever

PMID: 31776599 DOI: 10.1007/s00103-019-03061-2

Keywords: Pandemic Preparedness; Infectious Diseases; Emerging Diseases; Vaccines.