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Wilson R, Kovacs D, Crosby M, Ho A. Global Epidemiology and Seasonality of Human Seasonal Coronaviruses: A Systematic Review. Open Forum Infect Dis 2024; 11:ofae418. [PMID: 39113828 PMCID: PMC11304597 DOI: 10.1093/ofid/ofae418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Background We characterized the global epidemiology and seasonality of human coronaviruses (HCoVs) OC43, NL63, 229E, and HKU1. Methods In this systematic review, we searched MEDLINE, EMBASE, Web of Science, SCOPUS, CINAHL, and backward citations for studies published until 1 September 2023. We included studies with ≥12 months of consecutive data and tested for ≥1 HCoV species. Case reports, review articles, animal studies, studies focusing on SARS-CoV-1, SARS-CoV-2, and/or Middle East respiratory syndrome, and those including <100 cases were excluded. Study quality and risk of bias were assessed using Joanna Briggs Institute Critical Appraisal Checklist tools. We reported the prevalence of all HCoVs and individual species. Seasonality was reported for studies that included ≥100 HCoVs annually. This study is registered with PROSPERO, CRD42022330902. Results A total of 201 studies (1 819 320 samples) from 68 countries were included. A high proportion were from China (19.4%; n = 39), whereas the Southern Hemisphere was underrepresented. Most were case series (77.1%, n = 155) with samples from secondary care (74.1%, n = 149). Seventeen (8.5%) studies included asymptomatic controls, whereas 76 (37.8%) reported results for all 4 HCoV species. Overall, OC43 was the most prevalent HCoV. Median test positivity of OC43 and NL63 was higher in children, and 229E and HKU1 in adults. Among 18 studies that described seasonality (17 from the Northern Hemisphere), circulation of all HCoVs mostly peaked during cold months. Conclusions In our comprehensive review, few studies reported the prevalence of individual HCoVs or seasonality. Further research on the burden and circulation of HCoVs is needed, particularly from Africa, South Asia, and Central/South America.
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Affiliation(s)
- Rory Wilson
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Dory Kovacs
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mairi Crosby
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
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Jiang X, Yang D, Feng L, Zhu Y, Wang M, Feng Y, Bai C, Fang H. Contrastive learning with token projection for Omicron pneumonia identification from few-shot chest CT images. Front Med (Lausanne) 2024; 11:1360143. [PMID: 38756944 PMCID: PMC11096503 DOI: 10.3389/fmed.2024.1360143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Deep learning-based methods can promote and save critical time for the diagnosis of pneumonia from computed tomography (CT) images of the chest, where the methods usually rely on large amounts of labeled data to learn good visual representations. However, medical images are difficult to obtain and need to be labeled by professional radiologists. Methods To address this issue, a novel contrastive learning model with token projection, namely CoTP, is proposed for improving the diagnostic quality of few-shot chest CT images. Specifically, (1) we utilize solely unlabeled data for fitting CoTP, along with a small number of labeled samples for fine-tuning, (2) we present a new Omicron dataset and modify the data augmentation strategy, i.e., random Poisson noise perturbation for the CT interpretation task, and (3) token projection is utilized to further improve the quality of the global visual representations. Results The ResNet50 pre-trained by CoTP attained accuracy (ACC) of 92.35%, sensitivity (SEN) of 92.96%, precision (PRE) of 91.54%, and the area under the receiver-operating characteristics curve (AUC) of 98.90% on the presented Omicron dataset. On the contrary, the ResNet50 without pre-training achieved ACC, SEN, PRE, and AUC of 77.61, 77.90, 76.69, and 85.66%, respectively. Conclusion Extensive experiments reveal that a model pre-trained by CoTP greatly outperforms that without pre-training. The CoTP can improve the efficacy of diagnosis and reduce the heavy workload of radiologists for screening of Omicron pneumonia.
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Affiliation(s)
- Xiaoben Jiang
- School of Information Science and Technology, East China University of Science and Technology, Shanghai, China
| | - Dawei Yang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Internet of Things for Respiratory Medicine, Shanghai, China
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
| | - Li Feng
- Department of Nursing, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Zhu
- School of Information Science and Technology, East China University of Science and Technology, Shanghai, China
| | - Mingliang Wang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yinzhou Feng
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunxue Bai
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Internet of Things for Respiratory Medicine, Shanghai, China
| | - Hao Fang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Anesthesiology, Shanghai Geriatric Medical Center, Shanghai, China
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Sidorenko VS, Cohen I, Dorjee K, Minetti CA, Remeta DP, Gao J, Potapova I, Wang HZ, Hearing J, Yen WY, Kim HK, Hashimoto K, Moriya M, Dickman KG, Yin X, Garcia-Diaz M, Chennamshetti R, Bonala R, Johnson F, Waldeck AL, Gupta R, Li C, Breslauer KJ, Grollman AP, Rosenquist TA. Mechanisms of antiviral action and toxicities of ipecac alkaloids: Emetine and dehydroemetine exhibit anti-coronaviral activities at non-cardiotoxic concentrations. Virus Res 2024; 341:199322. [PMID: 38228190 PMCID: PMC10831786 DOI: 10.1016/j.virusres.2024.199322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/18/2024]
Abstract
The emergence of highly infectious pathogens with their potential for triggering global pandemics necessitate the development of effective treatment strategies, including broad-spectrum antiviral therapies to safeguard human health. This study investigates the antiviral activity of emetine, dehydroemetine (DHE), and congeneric compounds against SARS-CoV-2 and HCoV-OC43, and evaluates their impact on the host cell. Concurrently, we assess the potential cardiotoxicity of these ipecac alkaloids. Significantly, our data reveal that emetine and the (-)-R,S isomer of 2,3-dehydroemetine (designated in this paper as DHE4) reduce viral growth at nanomolar concentrations (i.e., IC50 ∼ 50-100 nM), paralleling those required for inhibition of protein synthesis, while calcium channel blocking activity occurs at elevated concentrations (i.e., IC50 ∼ 40-60 µM). Our findings suggest that the antiviral mechanisms primarily involve disruption of host cell protein synthesis and is demonstrably stereoisomer specific. The prospect of a therapeutic window in which emetine or DHE4 inhibit viral propagation without cardiotoxicity renders these alkaloids viable candidates in strategies worthy of clinical investigation.
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Affiliation(s)
- Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ira Cohen
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Kunchok Dorjee
- Division of Infectious Diseases, John Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Conceição A Minetti
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - David P Remeta
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Junyuan Gao
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Irina Potapova
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Hong Zhan Wang
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Janet Hearing
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Wan-Yi Yen
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Hwan Keun Kim
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Keiji Hashimoto
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Masaaki Moriya
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kathleen G Dickman
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Xingyu Yin
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rajesh Chennamshetti
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Radha Bonala
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Francis Johnson
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Amanda L Waldeck
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pharmacy, Stony Brook University Hospital, Stony Brook, New York 11794, USA
| | - Ramesh Gupta
- ChemMaster International Inc., Happauge, New York 11788, USA
| | - Chaoping Li
- Chemistry Service Unit of Shanghai Haoyuan Chemexpress Co., Ltd., Shanghai, PR China 201203
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Arthur P Grollman
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Thomas A Rosenquist
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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Jia Z, Xue P, Gao R, Wang R, Zhao L, Zuo Z, Gao L, Han R, Yao H, Guo J, Xu J, Zhu Z, Wang J. Epidemiology of Influenza-like Illness and Respiratory Viral Etiology in Adult Patients in Taiyuan City, Shanxi Province, China between 2018 and 2019. Viruses 2023; 15:2176. [PMID: 38005853 PMCID: PMC10674265 DOI: 10.3390/v15112176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
To determine the epidemiological status of influenza and understand the distribution of common respiratory viruses in adult patients with influenza-like illness (ILI) cases in Taiyuan City, Shanxi Province, China, epidemiological data between 2018 and 2019 were retrieved from the China Influenza Surveillance Information System, and two sentinel ILI surveillance hospitals were selected for sample collection. All specimens were screened for influenza virus (IFV) and the other 14 common respiratory viruses using real-time polymerase chain reaction. The results of the 2-year ILI surveillance showed that 26,205 (1.37%) of the 1,907,869 outpatients and emergency patients presented with ILI, with an average annual incidence of 297.75 per 100,000 individuals, and ILI cases were predominant in children <15 years (21,348 patients, 81.47%). Of the 2713 specimens collected from adult patients with ILI, the overall detection rate of respiratory viruses was 20.13%, with IFV being the most frequently detected (11.79%) and at a relatively lower rate than other respiratory viruses. Further subtype analysis indicated an alternating or mixed prevalence of H1N1 (2009), H3N2, Victoria, and Yamagata subtypes. This study provides a baseline epidemiological characterization of ILI and highlights the need for a nationwide detection and surveillance system for multiple respiratory pathogens.
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Affiliation(s)
- Zhao Jia
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, China; (Z.J.); (P.X.); (R.G.); (H.Y.); (J.G.)
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Puna Xue
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, China; (Z.J.); (P.X.); (R.G.); (H.Y.); (J.G.)
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Ruihong Gao
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, China; (Z.J.); (P.X.); (R.G.); (H.Y.); (J.G.)
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Rui Wang
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Lifeng Zhao
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Zhihong Zuo
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Li Gao
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Rui Han
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Hong Yao
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, China; (Z.J.); (P.X.); (R.G.); (H.Y.); (J.G.)
| | - Jiane Guo
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, China; (Z.J.); (P.X.); (R.G.); (H.Y.); (J.G.)
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Jihong Xu
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
| | - Zhen Zhu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jitao Wang
- School of Public Health, Shanxi Medical University, 56 Xinjian South Road, Taiyuan 030001, China; (Z.J.); (P.X.); (R.G.); (H.Y.); (J.G.)
- Taiyuan Center for Disease Control and Prevention, No. 22, Huazhang West Street, Xiaodian District, Taiyuan 030032, China; (R.W.); (L.Z.); (Z.Z.); (L.G.); (R.H.); (J.X.)
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Marco L, Cambien G, Garcia M, Broutin L, Cateau E, Lariviere A, Castel O, Thevenot S, Bousseau A. [Respiratory infections: Additional transmission-based precautions in healthcare facilities]. Rev Mal Respir 2023; 40:572-603. [PMID: 37365075 DOI: 10.1016/j.rmr.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/04/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION In health care, measures against cross-transmission of microorganisms are codified by standard precautions, and if necessary, they are supplemented by additional precautions. STATE OF THE ART Several factors impact transmission of microorganisms via the respiratory route: size and quantity of the emitted particles, environmental conditions, nature and pathogenicity of the microorganisms, and degree of host receptivity. While some microorganisms necessitate additional airborne or droplet precautions, others do not. PROSPECTS For most microorganisms, transmission patterns are well-understood and transmission-based precautions are well-established. For others, measures to prevent cross-transmission in healthcare facilities remain under discussion. CONCLUSIONS Standard precautions are essential to the prevention of microorganism transmission. Understanding of the modalities of microorganism transmission is essential to implementation of additional transmission-based precautions, particularly in view of opting for appropriate respiratory protection.
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Affiliation(s)
- L Marco
- Unité d'hygiène hospitalière, département des agents infectieux, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France
| | - G Cambien
- Unité d'hygiène hospitalière, département des agents infectieux, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France; Inserm CIC 1402, université de Poitiers, CHU de Poitiers, 86021 Poitiers, France
| | - M Garcia
- Département des agents infectieux, laboratoire de virologie et mycobactériologie, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France; Laboratoire inflammation, tissus épithéliaux et cytokines, EA 4331, université de Poitiers, 86021 Poitiers, France
| | - L Broutin
- Département des agents infectieux, laboratoire de bactériologie, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France
| | - E Cateau
- Laboratoire écologie et biologie des interactions, UMR CNRS 7267, université de Poitiers, 86021 Poitiers, France; Département des agents infectieux, laboratoire de parasitologie et mycologie médicale, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France
| | - A Lariviere
- Département des agents infectieux, laboratoire de virologie et mycobactériologie, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France
| | - O Castel
- Unité d'hygiène hospitalière, département des agents infectieux, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France
| | - S Thevenot
- Unité d'hygiène hospitalière, département des agents infectieux, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France; Inserm CIC 1402, université de Poitiers, CHU de Poitiers, 86021 Poitiers, France
| | - A Bousseau
- Unité d'hygiène hospitalière, département des agents infectieux, pôle BIOSPHARM, CHU de Poitiers, 86021 Poitiers, France.
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Stoufer S, Demokritou M, Buckley D, Teska P, Moore MD. Evaluation of the ability of commercial disinfectants to degrade free nucleic acid commonly targeted using molecular diagnostics. J Hosp Infect 2023; 133:28-37. [PMID: 36565931 DOI: 10.1016/j.jhin.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Polymerase chain reaction (PCR) is an essential tool for rapid detection of pathogens, but is susceptible to cross-contamination by residual nucleic acid, leading to false-positive results. Adequate surface decontamination would help prevent this, but most protocols target infectious microbes rather than free nucleic acid. The aim of this study was to evaluate the ability of commercial surface disinfectants to degrade different representative classes of nucleic acid. METHODS Commercial surface disinfectants with various active ingredients, as well as 10% chlorine bleach, were tested. Nucleic acid was dried on to stainless steel coupons and treated with disinfectant for 0-4 min prior to neutralization and quantification by quantitative reverse transcription PCR. The effective disinfectants were also evaluated in the presence of organic load. RESULTS Only dilute chlorine bleach and the hypochlorite-based commercial disinfectant significantly degraded any type of free nucleic acid. Hydrogen-peroxide- and quaternary-ammonium-based disinfectants gave <1 log reduction after 4 min for all targets. Results were time-dependent for each target, which underscores the importance of adequate contact time. Organic load appeared to have little impact on the efficacy of hypochlorite-based disinfectants for nucleic acid degradation. CONCLUSIONS This study demonstrates the importance of proper selection and application of disinfectant to remove residual nucleic acid when processing samples for molecular diagnostic testing.
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Affiliation(s)
- S Stoufer
- Department of Food Science, University of Massachusetts, Amherst, MA, USA.
| | - M Demokritou
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | | | - P Teska
- Diversey Inc., Fort Mill, SC, USA
| | - M D Moore
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
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Wang Z, Jung S, Yeo D, Park S, Woo S, Seo Y, Hossain MI, Kim M, Choi C. Assessing the Removal Efficiency of Murine Norovirus 1, Hepatitis A Virus, and Human Coronavirus 229E on Dish Surfaces Through General Wash Program of Household Dishwasher. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:61-70. [PMID: 36595129 PMCID: PMC9807978 DOI: 10.1007/s12560-022-09546-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/26/2022] [Indexed: 05/25/2023]
Abstract
The performance of dishwashers in removing live viruses is an important informative value in practical applications. Since foodborne viruses are present in contaminated food surfaces and water environments. Insufficient washing of dishes typically makes a carrier of foodborne viruses. Dishwashers have shown excellent performance in removing bacterial pathogens, but very limited reports related to eliminate foodborne viruses on contaminated dish surfaces. Here, murine norovirus 1 (MNV-1), hepatitis A virus (HAV), and human coronavirus 229E (HCoV-229E) were experimentally inoculated on the dish surfaces (plate, rice bowl, and soup bowl). Plaque assay, 50% tissue culture infectious dose (TCID50), and real-time quantitative polymerase chain reaction (RT-qPCR) were conducted to determine their removal efficiency of them through the general wash program of household dishwashers. Using titration assay, MNV-1 and HAV were reduced by 7.44 and 6.57 log10 PFU/dish, and HCoV-229E was reduced by 6.43 log10 TCID50/dish through the general wash program, achieving a ≥ 99.999% reduction, respectively. Additionally, RT-qPCR results revealed that viral RNA of MNV-1 and HCoV-229E reduced 5.02 and 4.54 log10 genome copies/dish; in contrast, HAV was not detected on any dish surfaces. This study confirmed the performance of household dishwashers in removing pathogenic live viruses through the general wash program. However, residual viral RNA was not sufficiently removed. Further studies are needed to determine whether the viral RNA can be sufficiently removed using combination programs in household dishwashers.
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Affiliation(s)
- Zhaoqi Wang
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Soontag Jung
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Daseul Yeo
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Sunho Park
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Seoyoung Woo
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Yeeun Seo
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Md Iqbal Hossain
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Minji Kim
- Technology R&D Office, SK magic, Hwaseong, Gyeonggi-do, 18298, Republic of Korea
| | - Changsun Choi
- Department of Food and Nutrition, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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Report of HKU-1 coronavirus nosocomial cluster in a city hospital in Japan during the coronavirus disease 2019 (COVID-19) pandemic. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e18. [PMID: 36714282 PMCID: PMC9879862 DOI: 10.1017/ash.2022.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 01/18/2023]
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Zuurbier RP, Bogaert D, de Steenhuijsen Piters WAA, Arp K, Chu MLJN, Sanders EAM, van Houten MA. Asymptomatic Viral Presence in Early Life Precedes Recurrence of Respiratory Tract Infections. Pediatr Infect Dis J 2023; 42:59-65. [PMID: 36476532 DOI: 10.1097/inf.0000000000003732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Respiratory tract infections (RTIs) in infants are often caused by viruses. Although respiratory syncytial virus (RSV), influenza virus and human metapneumovirus (hMPV) can be considered the most pathogenic viruses in children, rhinovirus (RV) is often found in asymptomatic infants as well. Little is known about the health consequences of viral presence, especially early in life. We aimed to examine the dynamics of (a)symptomatic viral presence and relate early viral detection to susceptibility to RTIs in infants. METHODS In a prospective birth cohort of 117 infants, we tested 1304 nasopharyngeal samples obtained from 11 consecutive regular sampling moments, and during acute RTIs across the first year of life for 17 respiratory viruses by quantitative PCR. Associations between viral presence, viral (sub)type, viral load, viral co-detection and symptoms were tested by generalized estimating equation (GEE) models. RESULTS RV was the most detected virus. RV was negatively associated [GEE: adjusted odds ratio (aOR) 0.41 (95% CI 0.18-0.92)], and hMPV, RSV, parainfluenza 2 and 4 and human coronavirus HKU1 were positively associated with an acute RTI. Asymptomatic RV in early life was, however, associated with increased susceptibility to and recurrence of RTIs later in the first year of life (Kaplan-Meier survival analysis: P = 0.022). CONCLUSIONS Respiratory viruses, including the seasonal human coronaviruses, are often detected in infants, and are often asymptomatic. Early life RV presence is, though negatively associated with an acute RTI, associated with future susceptibility to and recurrence of RTIs. Further studies on potential ecologic or immunologic mechanisms are needed to understand these observations.
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Affiliation(s)
- Roy P Zuurbier
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, The Netherlands
| | - Debby Bogaert
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- Medical Research Council and University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kayleigh Arp
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Mei Ling J N Chu
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth A M Sanders
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, The Netherlands
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
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10
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Faye MN, Barry MA, Jallow MM, Wade SF, Mendy MP, Sy S, Fall A, Kiori DE, Ndiaye NK, Goudiaby D, Diamanka A, Niang MN, Dia N. Epidemiology of Non-SARS-CoV2 Human Coronaviruses (HCoVs) in People Presenting with Influenza-like Illness (ILI) or Severe Acute Respiratory Infections (SARI) in Senegal from 2012 to 2020. Viruses 2022; 15:20. [PMID: 36680061 PMCID: PMC9864203 DOI: 10.3390/v15010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
In addition to emerging coronaviruses (SARS-CoV, MERS, SARS-CoV-2), there are seasonal human coronaviruses (HCoVs): HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1. With a wide distribution around the world, HCoVs are usually associated with mild respiratory disease. In the elderly, young children and immunocompromised patients, more severe or even fatal respiratory infections may be observed. In Africa, data on seasonal HCoV are scarce. This retrospective study investigated the epidemiology and genetic diversity of seasonal HCoVs during nine consecutive years of influenza-like illness surveillance in Senegal. Nasopharyngeal swabs were collected from ILI outpatients or from SARI hospitalized patients. HCoVs were diagnosed by qRT-PCR and the positive samples were selected for molecular characterization. Among 9337 samples tested for HCoV, 406 (4.3%) were positive: 235 (57.9%) OC43, 102 (25.1%) NL63, 58 (14.3%) 229E and 17 (4.2%) HKU1. The four types circulated during the study period and a peak was noted between November and January. Children under five were the most affected. Co-infections were observed between HCoV types (1.2%) or with other viruses (76.1%). Genetically, HCoVs types showed diversity. The results highlighted that the impact of HCoVs must be taken into account in public health; monitoring them is therefore particularly necessary both in the most sensitive populations and in animals.
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Affiliation(s)
- Modeste Name Faye
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Mamadou Malado Jallow
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Serigne Fallou Wade
- Ecole Supérieure des Sciences Agricoles et de l’Alimentation (ES2A), Université Amadou Makhtar MBOW de Dakar (UAM), Dakar 12900, Senegal
| | - Marie Pedapa Mendy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Amary Fall
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Davy Evrard Kiori
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | | | - Deborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Arfang Diamanka
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | | | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
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11
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Petros BA, Paull JS, Tomkins-Tinch CH, Loftness BC, DeRuff KC, Nair P, Gionet GL, Benz A, Brock-Fisher T, Hughes M, Yurkovetskiy L, Mulaudzi S, Leenerman E, Nyalile T, Moreno GK, Specht I, Sani K, Adams G, Babet SV, Baron E, Blank JT, Boehm C, Botti-Lodovico Y, Brown J, Buisker AR, Burcham T, Chylek L, Cronan P, Dauphin A, Desreumaux V, Doss M, Flynn B, Gladden-Young A, Glennon O, Harmon HD, Hook TV, Kary A, King C, Loreth C, Marrs L, McQuade KJ, Milton TT, Mulford JM, Oba K, Pearlman L, Schifferli M, Schmidt MJ, Tandus GM, Tyler A, Vodzak ME, Krohn Bevill K, Colubri A, MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J, Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC. Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework. MED 2022; 3:883-900.e13. [PMID: 36198312 PMCID: PMC9482833 DOI: 10.1016/j.medj.2022.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Universities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University and introduce a SARS-CoV-2 surveillance and response framework. METHODS We analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and WiFi-based co-location data) alongside pathogen surveillance data (wastewater and diagnostic testing, and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy. We applied relative risk, multiple linear regression, and social network assortativity to identify attributes or behaviors associated with contracting SARS-CoV-2. To characterize SARS-CoV-2 transmission, we used viral sequencing, phylogenomic tools, and functional assays. FINDINGS Athletes, particularly those on high-contact teams, had the highest risk of testing positive. On average, individuals who tested positive had more contacts and longer interaction durations than individuals who never tested positive. The distribution of contacts per individual was overdispersed, although not as overdispersed as the distribution of phylogenomic descendants. Corroboration via technical replicates was essential for identification of wastewater mutations. CONCLUSIONS Based on our findings, we formulate a framework that combines tools into an integrated disease surveillance program that can be implemented in other congregate settings with limited resources. FUNDING This work was supported by the National Science Foundation, the Hertz Foundation, the National Institutes of Health, the Centers for Disease Control and Prevention, the Massachusetts Consortium on Pathogen Readiness, the Howard Hughes Medical Institute, the Flu Lab, and the Audacious Project.
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Affiliation(s)
- Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA 02115, USA; Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jillian S Paull
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Christopher H Tomkins-Tinch
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Bryn C Loftness
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA; Complex Systems and Data Science PhD Program, University of Vermont, Burlington, VT 05405, USA; Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA.
| | | | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Aaron Benz
- Degree Analytics, Inc., Austin, TX 78758, USA
| | | | | | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Shandukani Mulaudzi
- Harvard Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ivan Specht
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kian Sani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Simone V Babet
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Emily Baron
- COVIDCheck Colorado, LLC, Denver, CO 80202, USA
| | - Jesse T Blank
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Chloe Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Princeton University Molecular Biology Department, Princeton, NJ 08544, USA
| | | | - Jeremy Brown
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | | | - Lily Chylek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul Cronan
- Fathom Information Design, Boston, MA 02114, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Valentine Desreumaux
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Megan Doss
- Warrior Diagnostics, Inc., Loveland, CO 80538, USA
| | - Belinda Flynn
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | | | | | - Thomas V Hook
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Anton Kary
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Clay King
- Department of Mathematics and Statistics, Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | - Libby Marrs
- Fathom Information Design, Boston, MA 02114, USA
| | - Kyle J McQuade
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Thorsen T Milton
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Jada M Mulford
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Kyle Oba
- Fathom Information Design, Boston, MA 02114, USA
| | - Leah Pearlman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Grace M Tandus
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Andy Tyler
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Megan E Vodzak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kelly Krohn Bevill
- Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Andres Colubri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - A Zeynep Ozsoy
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Eric Parrie
- COVIDCheck Colorado, LLC, Denver, CO 80202, USA
| | - Kari Sholtes
- Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ben Fry
- Fathom Information Design, Boston, MA 02114, USA
| | - Jeremy Luban
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John Marshall
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Amy Bronson
- Physician Assistant Program, Department of Kinesiology, Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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12
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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13
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Dorendorf A, Bachmann I, Spiegel M, Abd El Wahed A, Dame G, Hufert F. Rapid detection of human coronavirus NL63 by isothermal reverse transcription recombinase polymerase amplification. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100115. [PMID: 36248766 PMCID: PMC9546502 DOI: 10.1016/j.jcvp.2022.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Background Human coronaviruses are one of the leading causes for respiratory tract infections and for frequent primary care consultation. The human coronavirus NL63 (HCoV..µNL63) is one representative of the seasonal coronaviruses and capable of infecting the upper and lower respiratory tract and causative agent for croup in children. Objectives For fast detection of HCoV-NL63, we developed an isothermal reverse transcription recombinase polymerase amplification (RT-RPA) assay. Study design The analytical sensitivities of the RT-RPA assay were identified for in vitro transcribed ribonucleic acid (RNA) and for genomic viral RNA from cell culture supernatant. Moreover, specificity was tested with nucleic acids from other human coronaviruses and a variety of clinically relevant respiratory viruses. Finally, a clinical nasopharyngeal swab sample with spiked genomic viral HCoV-NL63 RNA was analyzed. Results Our HCoV-NL63 RT-RPA assay is highly specific and has an analytical sensitivity of 13 RNA molecules/reaction for in vitro transcribed RNA. For genomic viral RNA from cell culture supernatant spiked into a clinical nasopharyngeal swab sample the assay...s analytical sensitivity is 170 RNA molecules/reaction. The assay shows amplification of the lowest detectable target copy number after 8 minutes and 7 minutes, respectively. Conclusions We were able to design a sensitive and specific RT-RPA assay for the detection of HCoV-NL63. Additionally, the assay is characterized by short duration, isothermal amplification, and simple instrumentation.
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Affiliation(s)
- Aline Dorendorf
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Martin Spiegel
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Frank Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
- Brandenburg University of Technology Cottbus, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of Brandenburg University of Technology Cottbus - Senftenberg, Brandenburg Medical School Theodor Fontane, Neuruppin and University of Potsdam, Potsdam, Germany
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14
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Self-collected gargle fluids and nasopharyngeal swabs as a strategy for molecular diagnostics of respiratory viruses. JOURNAL OF CLINICAL VIROLOGY PLUS 2022. [DOI: 10.1016/j.jcvp.2022.100116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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15
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Joshi M, Mohandas S, Prasad S, Shinde M, Chavan N, Yadav PD, Lavania M. Lack of evidence of viability and infectivity of SARS-CoV-2 in the fecal specimens of COVID-19 patients. Front Public Health 2022; 10:1030249. [PMID: 36339137 PMCID: PMC9632423 DOI: 10.3389/fpubh.2022.1030249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 09/27/2022] [Indexed: 01/29/2023] Open
Abstract
SARS-CoV-2 can be shed in feces and can enter sewage systems. In order to implement effective control measures and identify new channels of transmission, it is essential to identify the presence of infectious virus particles in feces and sewage. In this study, we attempt to utilize Molecular techniques, cell cultures and animal models to find out the infectivity of SARS-CoV-2 in the feces of COVID-19 patients. Our findings exclude the presence of infectious virus particles, suggesting that fecal-oral transmission may not be the main mode of transmission. Larger-scale initiatives are nevertheless required, particularly considering the emergence of new viral strains.
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Affiliation(s)
- Madhuri Joshi
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Sreelekshmy Mohandas
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India
| | - Sharda Prasad
- Electron Microscopy and Histopathology Group, ICMR-National Institute of Virology, Pune, India
| | - Manohar Shinde
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Nutan Chavan
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Pragya D. Yadav
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India,*Correspondence: Pragya D. Yadav
| | - Mallika Lavania
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India,Mallika Lavania
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16
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Translational feasibility and efficacy of nasal photodynamic disinfection of SARS-CoV-2. Sci Rep 2022; 12:14438. [PMID: 36002557 PMCID: PMC9400568 DOI: 10.1038/s41598-022-18513-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 08/11/2022] [Indexed: 12/15/2022] Open
Abstract
The lack of therapeutic options to fight Covid-19 has contributed to the current global pandemic. Despite the emergence of effective vaccines, development of broad-spectrum antiviral treatment remains a significant challenge, in which antimicrobial photodynamic therapy (aPDT) may play a role, especially at early stages of infection. aPDT of the nares with methylene blue (MB) and non-thermal light has been successfully utilized to inactivate both bacterial and viral pathogens in the perioperative setting. Here, we investigated the effect of MB-aPDT to inactivate human betacoronavirus OC43 and SARS-CoV-2 in vitro and in a proof-of-principle COVID-19 clinical trial to test, in a variety of settings, the practicality, technical feasibility, and short-term efficacy of the method. aPDT yielded inactivation of up to 6-Logs in vitro, as measured by RT-qPCR and infectivity assay. From a photo-physics perspective, the in vitro results suggest that the response is not dependent on the virus itself, motivating potential use of aPDT for local destruction of SARS-CoV-2 and its variants. In the clinical trial we observed variable effects on viral RNA in nasal-swab samples as assessed by RT-qPCR attributed to aPDT-induced RNA fragmentation causing falsely-elevated counts. However, the viral infectivity in clinical nares swabs was reduced in 90% of samples and undetectable in 70% of samples. This is the first demonstration based on quantitative clinical viral infectivity measurements that MB-aPDT is a safe, easily delivered and effective front-line technique that can reduce local SARS-CoV-2 viral load.
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Zhang Z, Li D, Wang X, Wang Y, Lin J, Jiang S, Wu Z, He Y, Gao X, Zhu Z, Xiao Y, Qu Z, Li Y. Rapid detection of viruses: Based on silver nanoparticles modified with bromine ions and acetonitrile. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2022; 438:135589. [PMID: 35261557 PMCID: PMC8890791 DOI: 10.1016/j.cej.2022.135589] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 05/02/2023]
Abstract
Nearly 200 million people have been diagnosed with COVID-19 since the outbreak in 2019, and this disease has claimed more than 5 million lives worldwide. Currently, researchers are focusing on vaccine development and the search for an effective strategy to control the infection source. This work designed a detection platform based on Surface-Enhanced Raman Spectroscopy (SERS) by introducing acetonitrile and calcium ions into the silver nanoparticle reinforced substrate system to realize the rapid detection of novel coronavirus. Acetonitrile may amplify the calcium-induced hot spots of silver nanoparticles and significantly enhanced the stability of silver nanoparticles. It also elicited highly sensitive SERS signals of the virus. This approach allowed us to capture the characteristic SERS signals of SARS-CoV-2, Human Adenovirus 3, and H1N1 influenza virus molecules at a concentration of 100 copies/test (PFU/test) with upstanding reproduction and signal-to-noise ratio. Machine learning recognition technology was employed to qualitatively distinguish the three virus molecules with 1000 groups of spectra of each virus. Acetonitrile is a potent internal marker in regulating the signal intensity of virus molecules in saliva and serum. Thus, we used the SERS peak intensity to quantify the virus content in saliva and serum. The results demonstrated a satisfactory linear relationship between peak intensity and protein concentration. Collectively, this rapid detection method has a broad application prospect in clinical diagnosis of viruses, management of emergent viral infectious diseases, and exploration of the interaction between viruses and host cells.
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Affiliation(s)
- Zhe Zhang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Dan Li
- Institute of Physics, Guizhou University, Guiyang City, Guizhou Province 550025, PR China
| | - Xiaotong Wang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Yunpeng Wang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Jingyi Lin
- The Fourth Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
| | - Shen Jiang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Zheng Wu
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Yingying He
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Xin Gao
- Institute of Physics, Guizhou University, Guiyang City, Guizhou Province 550025, PR China
| | - Zhuo Zhu
- The Second Hospital of Jilin University, Jilin University, Changchun City, Jilin Province 130041, PR China
| | - Yanlong Xiao
- The Second Hospital of Jilin University, Jilin University, Changchun City, Jilin Province 130041, PR China
| | - Zhangyi Qu
- College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
| | - Yang Li
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
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Chhetri BK, Tedbury PR, Sweeney-Jones AM, Mani L, Soapi K, Manfredi C, Sorscher E, Sarafianos SG, Kubanek J. Marine Natural Products as Leads against SARS-CoV-2 Infection. JOURNAL OF NATURAL PRODUCTS 2022; 85:657-665. [PMID: 35290044 PMCID: PMC8936055 DOI: 10.1021/acs.jnatprod.2c00015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Indexed: 05/13/2023]
Abstract
Since early 2020, disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic, causing millions of infections and deaths worldwide. Despite rapid deployment of effective vaccines, it is apparent that the global community lacks multipronged interventions to combat viral infection and disease. A major limitation is the paucity of antiviral drug options representing diverse molecular scaffolds and mechanisms of action. Here we report the antiviral activities of three distinct marine natural products─homofascaplysin A (1), (+)-aureol (2), and bromophycolide A (3)─evidenced by their ability to inhibit SARS-CoV-2 replication at concentrations that are nontoxic toward human airway epithelial cells. These compounds stand as promising candidates for further exploration toward the discovery of novel drug leads against SARS-CoV-2.
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Affiliation(s)
- Bhuwan Khatri Chhetri
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Luke Mani
- Institute of Applied Sciences, University of South Pacific, Suva, Fiji
| | - Katy Soapi
- Institute of Applied Sciences, University of South Pacific, Suva, Fiji
| | - Candela Manfredi
- Department of Pediatrics, Division of Pulmonary Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric Sorscher
- Department of Pediatrics, Division of Pulmonary Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Julia Kubanek
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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19
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Gosavi D, Cheatham B, Sztuba-Solinska J. Label-Free Detection of Human Coronaviruses in Infected Cells Using Enhanced Darkfield Hyperspectral Microscopy (EDHM). J Imaging 2022; 8:24. [PMID: 35200727 PMCID: PMC8874371 DOI: 10.3390/jimaging8020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
Human coronaviruses (HCoV) are causative agents of mild to severe intestinal and respiratory infections in humans. In the last 15 years, we have witnessed the emergence of three zoonotic, highly pathogenic HCoVs. Thus, early and accurate detection of these viral pathogens is essential for preventing transmission and providing timely treatment and monitoring of drug resistance. Herein, we applied enhanced darkfield hyperspectral microscopy (EDHM), a novel non-invasive, label-free diagnostic tool, to rapidly and accurately identify two strains of HCoVs, i.e., OC43 and 229E. The EDHM technology allows collecting the optical image with spectral and spatial details in a single measurement without direct contact between the specimen and the sensor. Thus, it can directly map spectral signatures specific for a given viral strain in a complex biological milieu. Our study demonstrated distinct spectral patterns for HCoV-OC43 and HCoV-229E virions in the solution, serving as distinguishable parameters for their differentiation. Furthermore, spectral signatures obtained for both HCoV strains in the infected cells displayed a considerable peak wavelength shift compared to the uninfected cell, indicating that the EDHM is applicable to detect HCoV infection in mammalian cells.
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Affiliation(s)
- Devadatta Gosavi
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL 36849, USA;
| | - Byron Cheatham
- Cytoviva, Inc., 570 Devall Drive Suite 301, Auburn, AL 36832, USA;
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL 36849, USA;
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20
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Bukkitgar SD, Shetti NP, Aminabhavi TM. Electrochemical investigations for COVID-19 detection-A comparison with other viral detection methods. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 420:127575. [PMID: 33162783 PMCID: PMC7605744 DOI: 10.1016/j.cej.2020.127575] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/07/2020] [Accepted: 10/26/2020] [Indexed: 05/02/2023]
Abstract
Virus-induced infection such as SARS-CoV-2 is a serious threat to human health and the economic setback of the world. Continued advances in the development of technologies are required before the viruses undergo mutation. The low concentration of viruses in environmental samples makes the detection extremely challenging; simple, accurate and rapid detection methods are in urgent need. Of all the analytical techniques, electrochemical methods have the established capabilities to address the issues. Particularly, the integration of nanotechnology would allow miniature devices to be made available at the point-of-care. This review outlines the capabilities of electrochemical methods in conjunction with nanotechnology for the detection of SARS-CoV-2. Future directions and challenges of the electrochemical biosensors for pathogen detection are covered including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, and reusable biosensors for on-site monitoring, thereby providing low-cost and disposable biosensors.
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Key Words
- AIV H5N1, Avian influenza
- AIV, Avian influenza virus
- ASFV, African swine fever virus
- BVDV, Bovine viral diarrhea virus
- CGV, Chikungunya viruses
- CMV, Cucumber mosaic virus
- COVID-19
- CSFV, Classic swine fever virus
- CV, Cyclic voltammetry
- DAstV-1, Duck astrovirus 1
- DAstV-2, Duck astrovirus 2
- DENV, Dengue virus
- DEV, Duck enteritis virus
- DHAV-1, Duck hepatitis A virus 1
- DHAV-3, Duck hepatitis A virus 3
- DPV, Differential pulse voltammetry
- DRV-1, Duck reovirus 1
- DRV-2, Duck reovirus 2
- Detection
- EBV, Epstein-Barr virus
- EIS, Electric impedance spectroscopy
- EPC, External positive controls
- EV, Human enterovirus
- EV71, Human enterovirus 71
- Electrochemical sensor
- FMI SMOF, Fluorescence molecularly imprinted sensor based on a metal–organic framework
- GCE, Glassy carbon electrode
- GCFaV-1, Ginger chlorotic fleck associated virus 1
- GCFaV-2, Ginger chlorotic fleck-associated virus 2
- GEV VN-96, Gastroenteritis virus VN-96
- GPV, Goose parvovirus
- HHV, Human herpes virus 6
- HIAV, Human influenza A viruses
- HPB19, Human parvovirus B19
- HSV, Herpes simplex
- IAV, influenza A virus
- IEA, Interdigitated electrode array
- IMA, Interdigitated microelectrode array
- INAA, Isothermal nucleic acid amplification-based
- JEV, Japanese encephalitis virus
- LAMP, Loop-Mediated Isothermal Amplification
- LSV, Linear sweep voltammetry
- MERS, Middle East respiratory syndrome
- MIEC, Molecularly imprinted electrochemiluminescence
- MNV, Murine norovirus
- MeV, Measles virus
- NNV, Nervous necrosis virus
- Nanotechnology
- PBoV, Porcine bocavirus
- PCNAME, Pt-coated nanostructured alumina membrane electrode
- PCR
- PCRLFS, Polymerase Chain Reaction with a lateral flow strip with a lateral flow strip
- PCV, Porcine circovirus 3
- PEDV, Porcine epidemic diarrhoea virus
- PRRSV, porcine reproductive and respiratory syndrome virus
- PSV, Pseudorabies virus
- RCA, Rolling circle amplification
- RGO, Reduced graphene oxide
- RT-LAMP-VF, RT-LAMP and a vertical flow visualization strip
- RV, Rubella virus
- SARS, Severe acute respiratory syndrome
- SIVH1N1, Swine influenza virus
- SWV, Square wave voltammetry
- TGEV, transmissible gastroenteritis coronavirus
- TMUV, Tembusu virus
- USEGFET, Ultra-sensitive electrolyte-gated field-effect transistor
- VZV, Varicella-zoster virus
- VZV, varicella-Zoster virus
- Viruses
- ZV, Zika virus
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Affiliation(s)
- Shikandar D Bukkitgar
- Centre for Electrochemical Science and Materials, Department of Chemistry, K.L.E. Institute of Technology, Gokul, Hubballi 580030, Karnataka, India
| | - Nagaraj P Shetti
- Centre for Electrochemical Science and Materials, Department of Chemistry, K.L.E. Institute of Technology, Gokul, Hubballi 580030, Karnataka, India
| | - Tejraj M Aminabhavi
- Pharmaceutical Engineering, Soniya College of Pharmacy, Dharwad 580-007, India
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21
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Zocchi E, Terrazzano G. COVID-19: why not learn from the past? Front Med 2021; 15:776-781. [PMID: 34463906 PMCID: PMC8407128 DOI: 10.1007/s11684-021-0883-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/23/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Elena Zocchi
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy.
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22
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Sampson AT, Heeney J, Cantoni D, Ferrari M, Sans MS, George C, Di Genova C, Mayora Neto M, Einhauser S, Asbach B, Wagner R, Baxendale H, Temperton N, Carnell G. Coronavirus Pseudotypes for All Circulating Human Coronaviruses for Quantification of Cross-Neutralizing Antibody Responses. Viruses 2021; 13:1579. [PMID: 34452443 PMCID: PMC8402765 DOI: 10.3390/v13081579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/17/2021] [Accepted: 08/01/2021] [Indexed: 12/23/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 is the seventh identified human coronavirus. Understanding the extent of pre-existing immunity induced by seropositivity to endemic seasonal coronaviruses and the impact of cross-reactivity on COVID-19 disease progression remains a key research question in immunity to SARS-CoV-2 and the immunopathology of COVID-2019 disease. This paper describes a panel of lentiviral pseudotypes bearing the spike (S) proteins for each of the seven human coronaviruses (HCoVs), generated under similar conditions optimized for high titre production allowing a high-throughput investigation of antibody neutralization breadth. Optimal production conditions and most readily available permissive target cell lines were determined for spike-mediated entry by each HCoV pseudotype: SARS-CoV-1, SARS-CoV-2 and HCoV-NL63 best transduced HEK293T/17 cells transfected with ACE2 and TMPRSS2, HCoV-229E and MERS-CoV preferentially entered HUH7 cells, and CHO cells were most permissive for the seasonal betacoronavirus HCoV-HKU1. Entry of ACE2 using pseudotypes was enhanced by ACE2 and TMPRSS2 expression in target cells, whilst TMPRSS2 transfection rendered HEK293T/17 cells permissive for HCoV-HKU1 and HCoV-OC43 entry. Additionally, pseudotype viruses were produced bearing additional coronavirus surface proteins, including the SARS-CoV-2 Envelope (E) and Membrane (M) proteins and HCoV-OC43/HCoV-HKU1 Haemagglutinin-Esterase (HE) proteins. This panel of lentiviral pseudotypes provides a safe, rapidly quantifiable and high-throughput tool for serological comparison of pan-coronavirus neutralizing responses; this can be used to elucidate antibody dynamics against individual coronaviruses and the effects of antibody cross-reactivity on clinical outcome following natural infection or vaccination.
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Affiliation(s)
- Alexander Thomas Sampson
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.H.); (M.F.); (M.S.S.); (C.G.); (G.C.)
| | - Jonathan Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.H.); (M.F.); (M.S.S.); (C.G.); (G.C.)
- DIOSynVax Ltd., Cambridge CB3 0ES, UK
| | - Diego Cantoni
- Viral Pseudotype Unit, University of Kent, Chatham ME4 4TB, UK; (D.C.); (C.D.G.); (M.M.N.); (N.T.)
| | - Matteo Ferrari
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.H.); (M.F.); (M.S.S.); (C.G.); (G.C.)
- DIOSynVax Ltd., Cambridge CB3 0ES, UK
| | - Maria Suau Sans
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.H.); (M.F.); (M.S.S.); (C.G.); (G.C.)
| | - Charlotte George
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.H.); (M.F.); (M.S.S.); (C.G.); (G.C.)
| | - Cecilia Di Genova
- Viral Pseudotype Unit, University of Kent, Chatham ME4 4TB, UK; (D.C.); (C.D.G.); (M.M.N.); (N.T.)
| | - Martin Mayora Neto
- Viral Pseudotype Unit, University of Kent, Chatham ME4 4TB, UK; (D.C.); (C.D.G.); (M.M.N.); (N.T.)
| | - Sebastian Einhauser
- Institute for Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany; (S.E.); (B.A.); (R.W.)
| | - Benedikt Asbach
- Institute for Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany; (S.E.); (B.A.); (R.W.)
| | - Ralf Wagner
- Institute for Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany; (S.E.); (B.A.); (R.W.)
- Institute for Clinical Microbiology and Hygiene, University Hospital, 93053 Regensburg, Germany
| | - Helen Baxendale
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK;
| | - Nigel Temperton
- Viral Pseudotype Unit, University of Kent, Chatham ME4 4TB, UK; (D.C.); (C.D.G.); (M.M.N.); (N.T.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.H.); (M.F.); (M.S.S.); (C.G.); (G.C.)
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23
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Corman VM, Haage VC, Bleicker T, Schmidt ML, Mühlemann B, Zuchowski M, Jo WK, Tscheak P, Möncke-Buchner E, Müller MA, Krumbholz A, Drexler JF, Drosten C. Comparison of seven commercial SARS-CoV-2 rapid point-of-care antigen tests: a single-centre laboratory evaluation study. THE LANCET. MICROBE 2021; 2:e311-e319. [PMID: 33846704 PMCID: PMC8026170 DOI: 10.1016/s2666-5247(21)00056-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Antigen point-of-care tests (AgPOCTs) can accelerate SARS-CoV-2 testing. As some AgPOCTs have become available, interest is growing in their utility and performance. Here we aimed to compare the analytical sensitivity and specificity of seven commercially available AgPOCT devices. METHODS In a single-centre, laboratory evaluation study, we compared AgPOCT products from seven suppliers: the Abbott Panbio COVID-19 Ag Rapid Test, the RapiGEN BIOCREDIT COVID-19 Ag, the Healgen Coronavirus Ag Rapid Test Cassette (Swab), the Coris BioConcept COVID-19 Ag Respi-Strip, the R-Biopharm RIDA QUICK SARS-CoV-2 Antigen, the nal von minden NADAL COVID-19 Ag Test, and the Roche-SD Biosensor SARS-CoV Rapid Antigen Test. Tests were evaluated on recombinant SARS-CoV-2 nucleoprotein, cultured endemic and emerging coronaviruses, stored respiratory samples with known SARS-CoV-2 viral loads, stored samples from patients with respiratory pathogens other than SARS-CoV-2, and self-sampled swabs from healthy volunteers. We estimated analytical sensitivity in terms of approximate viral concentrations (quantified by real-time RT-PCR) that yielded positive AgPOCT results, and specificity in terms of propensity to generate false-positive results. FINDINGS In 138 clinical samples with quantified SARS-CoV-2 viral load, the 95% limit of detection (concentration at which 95% of test results were positive) in six of seven AgPOCT products ranged between 2·07 × 106 and 2·86 × 107 copies per swab, with an outlier (RapiGEN) at 1·57 × 1010 copies per swab. The assays showed no cross-reactivity towards cell culture or tissue culture supernatants containing any of the four endemic human coronaviruses (HCoV‑229E, HCoV‑NL63, HCoV‑OC43, or HCoV‑HKU1) or MERS-CoV, with the exception of the Healgen assay in one repeat test on HCoV-HKU1 supernatant. SARS-CoV was cross-detected by all assays. Cumulative specificities among stored clinical samples with non-SARS-CoV-2 infections (n=100) and self-samples from healthy volunteers (n=35; cumulative sample n=135) ranged between 98·5% (95% CI 94·2-99·7) and 100·0% (97·2-100·0) in five products, with two outliers at 94·8% (89·2-97·7; R-Biopharm) and 88·9% (82·1-93·4; Healgen). False-positive results did not appear to be associated with any specific respiratory pathogen. INTERPRETATION The sensitivity range of most AgPOCTs overlaps with SARS-CoV-2 viral loads typically observed in the first week of symptoms, which marks the infectious period in most patients. The AgPOCTs with limit of detections that approximate virus concentrations at which patients are infectious might enable shortcuts in decision making in various areas of health care and public health. FUNDING EU's Horizon 2020 research and innovation programme, German Ministry of Research, German Federal Ministry for Economic Affairs and Energy, German Ministry of Health, and Bill & Melinda Gates Foundation.
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Affiliation(s)
- Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany
| | - Verena Claudia Haage
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marie Luisa Schmidt
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | - Wendy K Jo
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Patricia Tscheak
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elisabeth Möncke-Buchner
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrecht University and University Medical Center Schleswig-Holstein, Kiel, Germany; Labor Dr Krause und Kollegen MVZ, Kiel, Germany
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany.
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24
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Nicol MP, MacGinty R, Workman L, Stadler JAM, Myer L, Allen V, Ah Tow Edries L, Zar HJ. A Longitudinal Study of the Epidemiology of Seasonal Coronaviruses in an African Birth Cohort. J Pediatric Infect Dis Soc 2021; 10:607-614. [PMID: 33528016 PMCID: PMC7928775 DOI: 10.1093/jpids/piaa168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Since non-epidemic, seasonal human coronaviruses (sHCoV) commonly infect children, an improved understanding of the epidemiology of these infections may offer insights into the context of severe acute respiratory syndrome (SARS)-CoV-2. We investigated the epidemiology of sHCoV infection during the first year of life, including risk factors and association with lower respiratory tract infection (LRTI). METHODS We conducted a nested case-control study of infants enrolled in a birth cohort near Cape Town, South Africa, from 2012 to 2015. LRTI surveillance was implemented, and nasopharyngeal swabs were collected fortnightly over infancy. Quantitative PCR detected respiratory pathogens, including coronaviruses-229E, -NL63, -OC43, and -HKU1. Swabs were tested from infants at the time of LRTI and from the 90 days prior as well as from age-matched control infants from the cohort over the equivalent period. RESULTS In total, 885 infants were included, among whom 464 LRTI events occurred. Of the 4751 samples tested for sHCoV, 9% tested positive, with HCoV-NL63 the most common. Seasonal HCoV detection was associated with LRTI; this association was strongest for coronavirus-OC43, which was also found in all sHCoV-associated hospitalizations. Birth in winter was associated with sHCoV-LRTI, but there were no clear seasonal differences in detection. Co-detection of Streptococcus pneumoniae was weakly associated with sHCoV-LRTI (odds ratio: 1.8; 95% confidence interval: 0.9-3.6); detection of other respiratory viruses or bacteria was not associated with sHCoV status. CONCLUSIONS Seasonal HCoV infections were common and associated with LRTI, particularly sHCoV-OC43, which is most closely related to the SARS group of coronaviruses. Interactions of coronaviruses with bacteria in the pathogenesis of LRTI require further study.
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Affiliation(s)
- Mark P Nicol
- Division of Infection and Immunity, School of Biomedical Sciences, Faculty of Health Sciences, University of Western Australia, Perth, Australia
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rae MacGinty
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| | - Jacob A M Stadler
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| | - Landon Myer
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Veronica Allen
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Lemese Ah Tow Edries
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
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25
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Benzigar MR, Bhattacharjee R, Baharfar M, Liu G. Current methods for diagnosis of human coronaviruses: pros and cons. Anal Bioanal Chem 2021; 413:2311-2330. [PMID: 33219449 PMCID: PMC7679240 DOI: 10.1007/s00216-020-03046-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/14/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022]
Abstract
The current global fight against coronavirus disease (COVID-19) to flatten the transmission curve is put forth by the World Health Organization (WHO) as there is no immediate diagnosis or cure for COVID-19 so far. In order to stop the spread, researchers worldwide are working around the clock aiming to develop reliable tools for early diagnosis of severe acute respiratory syndrome (SARS-CoV-2) understanding the infection path and mechanisms. Currently, nucleic acid-based molecular diagnosis (real-time reverse transcription polymerase chain reaction (RT-PCR) test) is considered the gold standard for early diagnosis of SARS-CoV-2. Antibody-based serology detection is ineffective for the purpose of early diagnosis, but a potential tool for serosurveys, providing people with immune certificates for clearance from COVID-19 infection. Meanwhile, there are various blooming methods developed these days. In this review, we summarise different types of coronavirus discovered which can be transmitted between human beings. Methods used for diagnosis of the discovered human coronavirus (SARS, MERS, COVID-19) including nucleic acid detection, gene sequencing, antibody detection, antigen detection, and clinical diagnosis are presented. Their merits, demerits and prospects are discussed which can help the researchers to develop new generation of advanced diagnostic tools for accurate and effective control of human coronavirus transmission in the communities and hospitals.
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Affiliation(s)
- Mercy R Benzigar
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ripon Bhattacharjee
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mahroo Baharfar
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Guozhen Liu
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia.
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Ramani R, Laplante JM, Church TM, Farrell GM, Lamson DM, St George K. CACO-2 cells: A continuous cell line with sensitive and broad-spectrum utility for respiratory virus culture. J Virol Methods 2021; 293:114120. [PMID: 33676967 DOI: 10.1016/j.jviromet.2021.114120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Primary rhesus monkey kidney cells (RhMK) can be used for the detection of respiratory viruses, including influenza and parainfluenza. The human colon adeno-carcinoma cell line, CACO-2, has been previously used for the growth of multiple influenza viruses, including seasonal, novel and avian lineages. OBJECTIVE We compared CACO-2, Madin-Darby Canine Kidney (MDCK), and RhMK cells for the isolation of viruses from patients presenting with influenza like-illness (ILI). STUDY DESIGN Nasopharyngeal specimens from patients with ILI in primary care settings were processed for conventional viral culture in MDCK, RhMK, and CACO-2. Cells were examined microscopically for cytopathic effect (CPE) and confirmatory testing included immunofluorescent antigen (IFA) detection and real-time RT-PCR. Additionally, 16 specimens positive for respiratory syncytial virus (RSV) by PCR were inoculated on CACO-2 cells. Statistical analysis was done using Chi-square test with IBM Statistical Program. RESULTS Of 1031 respiratory specimens inoculated, viruses were isolated and confirmed from 331 (32.1 %) in MDCK cells, 304 (29.5 %) in RhMk cells, and 433 (42.0 %) in CACO-2 cells. These included influenza A/(H1N1)pdm09, influenza A(H3N2), influenza B, parainfluenza virus (PIV) types 1, 2, and 3, human coronavirus 229E (CoV-229E), human adenovirus (HAdV), herpes simplex virus 1 (HSV 1), and enterovirus (EV). Influenza A viruses grew best in the CACO-2 cell line. Time to observation of CPE was similar for all three cell types but unlike RhMK and MDCK cells, virus-specific morphological changes were indistinguishable in CACO-2 cells. None of the 16 specimens positive for RSV by PCR grew on CACO-2 cells. CONCLUSIONS The overall respiratory virus culture isolation rate in CACO-2 cells was significantly higher than that in RhMK or MDCK cells (p < 0.05). CACO-2 cells also supported the growth of some viruses that did not grow in either RhMK or MDCK cells. Except for RSV, CACO-2 cells provide a worthwhile addition to culture algorithms for respiratory specimens.
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Affiliation(s)
- Rama Ramani
- Laboratory of Viral Diseases, Wadsworth Center, Albany, NY, USA
| | | | | | | | - Daryl M Lamson
- Laboratory of Viral Diseases, Wadsworth Center, Albany, NY, USA
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Das Mukhopadhyay C, Sharma P, Sinha K, Rajarshi K. Recent trends in analytical and digital techniques for the detection of the SARS-Cov-2. Biophys Chem 2021; 270:106538. [PMID: 33418105 PMCID: PMC7768211 DOI: 10.1016/j.bpc.2020.106538] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/30/2020] [Accepted: 12/24/2020] [Indexed: 12/26/2022]
Abstract
The current global outbreak of COVID-19 due to SARS-CoV-2 is an unprecedented humanitarian crisis. Considering the gravity of its impact there is an immediate need to develop a detection technique that is sensitive, specific, fast, and affordable for the clinical diagnosis of the disease. Real time Polymerase Chain Reaction (RT-PCR)-based detection platforms are contemplated to be the gold standard to detect viral RNA. However, that may be susceptible to errors, and there is a risk of obtaining false results, which ultimately compromises the strategy of efficient disease management. Several modern techniques exhibiting assured results with enhanced sensitivity and specificity against the SARS-CoV-2 associated viral components or immune response against it have been developed and may be implemented. The review deals with the conventional RT-PCR detection techniques and compares them to other detection platforms viz., biosensor based detection of antigens, fluorescent or colorimetric detection systems including CRISPR-Cas 13 based SHERLOCK kit, CRISPR Cas-9 based FELUDA test kit, CRISPR DETECTR kit, Next Generation Sequencing or microarray-based kits. These modern techniques are great as a point of care detection methods but should be followed by RT PCR based detection for the confirmation of COVID-19 status.
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Affiliation(s)
- Chitrangada Das Mukhopadhyay
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India.
| | - Pramita Sharma
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
| | - Koel Sinha
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
| | - Keshav Rajarshi
- School of Community Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
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Narayanan S, Ritchey JC, Patil G, Narasaraju T, More S, Malayer J, Saliki J, Kaul A, Agarwal PK, Ramachandran A. SARS-CoV-2 Genomes From Oklahoma, United States. Front Genet 2021; 11:612571. [PMID: 33613621 PMCID: PMC7886813 DOI: 10.3389/fgene.2020.612571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/31/2020] [Indexed: 11/13/2022] Open
Abstract
Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study, we sequenced SARS-CoV-2 from five clinical samples obtained in Oklahoma, United States during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and four during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K, and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). Phylogenetic analysis of the genomes showed similarity to other SARS-CoV-2 viruses reported from across the globe. Structural characterization indicates that the mutations in S gene possibly influences conformational flexibility and motion of the spike protein, and the mutations in N gene are associated with disordered linker region within the nucleocapsid protein.
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Affiliation(s)
- Sai Narayanan
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - John C. Ritchey
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Girish Patil
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Teluguakula Narasaraju
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Sunil More
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Jerry Malayer
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Jeremiah Saliki
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Anil Kaul
- Center for Health Sciences, Oklahoma State University, Tulsa, OK, United States
| | - Pratul K. Agarwal
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- High-Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
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Coronavirus Surveillance in a Pediatric Population in Jordan From 2010 to 2013: A Prospective Viral Surveillance Study. Pediatr Infect Dis J 2021; 40:e12-e17. [PMID: 33165274 DOI: 10.1097/inf.0000000000002965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Human coronaviruses (HCoVs) are a significant cause of acute respiratory illness (ARI) in children; however, the role of HCoVs in ARI among hospitalized children in the Middle East is not well defined. METHODS Children under 2 years admitted with fever and/or respiratory symptoms were enrolled from 2010 to 2013 in Amman, Jordan. Nasal/throat swabs were collected and stored for testing. Demographic and clinical characteristics were collected through parent/guardian interviews and medical chart abstractions. Prior stored specimens were tested for HCoVs (HKU1, OC43, 229E and NL63) by qRT-PCR. RESULTS Of the 3168 children enrolled, 6.7% were HCoVs-positive. Among HCoV-positive children, the median age was 3.8 (1.9-8.4) months, 59% were male, 14% were premature, 11% had underlying medical conditions and 76% had viral-codetection. The most common presenting symptoms were cough, fever, wheezing and shortness of breath. HCoVs were detected year-round, peaking in winter-spring months. Overall, 56%, 22%, 13% and 6% were OC43, NL63, HKU1 and 229E, respectively. There was no difference in disease severity between the species, except higher intensive care unit admission frequency in NL63-positive subjects. CONCLUSIONS HCoVs were detected in around 7% of children enrolled in our study. Despite HCoV detection in children with ARI with highest peaks in respiratory seasons, the actual burden and pathogenic role of HCoVs in ARI merits further evaluation given the high frequency of viral codetection.
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Dastidar MG, Roy S. Public health management during COVID-19 and applications of point-of-care based biomolecular detection approaches. ENVIRONMENTAL AND HEALTH MANAGEMENT OF NOVEL CORONAVIRUS DISEASE (COVID-19 ) 2021. [PMCID: PMC8237533 DOI: 10.1016/b978-0-323-85780-2.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The emergence of the novel human coronavirus, characterized as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a worldwide pandemic. The outbreak of SARS-CoV-2 was first reported at a local wet market in the city of Wuhan in the Hubei province of China at a local wet market. This virus is highly contagious, which gives it the potential for rapid transmission across the world. The transmission of SARS-CoV-2 can be triggered via respiratory droplets in the air from an infected individual to a healthy individual. Thus, to restrict the transmission of the virus, proper public health management and early diagnosis of infected individual is extremely essential. Considering this, the development of various point-of-care (POC) biomolecular assays lead to the importance of early diagnoses at a larger scale during this pandemic situation. Detecting a minimum level of specific target analytes to a particular disease with less instrumentation and minimum reagents, as well as immidiate outcomes, has appeared a challenging path for researchers. Apart from early-stage diagnosis, public awareness is also important to prevent the spread of the virus. Proper intensive care units, isolation rooms, maintaining hygiene, and wearing masks in public areas are necessary. In this chapter, we have discussed the public health management steps and current clinical diagnostics processes and various advanced technology including, molecular, serological, and nanobiosensing approaches for SARS-CoV-2 detection. Furthermore, we have highlighted the various challenges and limitations associated with health management and early diagnostics technologies during SARS-CoV-2 pandemic. Additionally, we have summarized various technical aspects of the development of such POC strategies including biomarkers selections, sensing platforms, unit fabrication, and device incorporation.
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Zenhausern R, Chen CH, Yoon JY. Microfluidic sample preparation for respiratory virus detection: A review. BIOMICROFLUIDICS 2021; 15:011503. [PMID: 33643510 PMCID: PMC7889292 DOI: 10.1063/5.0041089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/28/2021] [Indexed: 05/05/2023]
Abstract
Techniques used to prepare clinical samples have been perfected for use in diagnostic testing in a variety of clinical situations, e.g., to extract, concentrate, and purify respiratory virus particles. These techniques offer a high level of purity and concentration of target samples but require significant equipment and highly trained personnel to conduct, which is difficult to achieve in resource-limited environments where rapid testing and diagnostics are crucial for proper handling of respiratory viruses. Microfluidics has popularly been utilized toward rapid virus detection in resource-limited environments, where most devices focused on detection rather than sample preparation. Initial microfluidic prototypes have been hindered by their reliance on several off-chip preprocessing steps and external laboratory equipment. Recently, sample preparation methods have also been incorporated into microfluidics to conduct the virus detection in an all-in-one, automated manner. Extraction, concentration, and purification of viruses have been demonstrated in smaller volumes of samples and reagents, with no need for specialized training or complex machinery. Recent devices show the ability to function independently and efficiently to provide rapid, automated sample preparation as well as the detection of viral samples with high efficiency. In this review, methods of microfluidic sample preparation for the isolation and purification of viral samples are discussed, limitations of current systems are summarized, and potential advances are identified.
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Affiliation(s)
- Ryan Zenhausern
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
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Uhteg K, Carroll KC, Mostafa HH. Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus? Clin Lab Med 2020; 40:459-472. [PMID: 33121615 PMCID: PMC7414311 DOI: 10.1016/j.cll.2020.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.
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Cimolai N. Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses. Health Secur 2020; 19:195-208. [PMID: 33186086 DOI: 10.1089/hs.2020.0067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory coronaviruses that typically cause mild to moderate upper respiratory infections, similar to the common cold. They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications. These viruses are usually seasonal (with winter dominance) and affect nearly all age groups. The seasonal and annual variation in virus prevalence has implications for understanding the concept of acquired immunity and its persistence or diminution. Coronaviruses generally have outbreak potential in susceptible populations of any age, particularly in patients with comorbidities, who tend to have increased clinical disease. These 4 coronaviruses are often found in the context of what appears to be coinfection with other pathogens, but especially other viruses. If coronaviruses are not specifically tested for, the sole detection of a viral copathogen would suggest the pathogen is the causative agent, when a coronavirus may be culpable, or both. The detection of these viruses in circumstances where respiratory viruses are generally sought in clinical samples is, therefore, justified. These pathogens can be chronically shed from the respiratory tract, which is more likely to occur among immunocompromised and complicated patients. These viruses share the potential for genetic drift. The genome is among the largest of RNA viruses, and the capability of these viruses to further change is likely underestimated. Given the potential disease among humans, it is justified to search for effective antiviral chemotherapy for these viruses and to consider uses in niche situations should effective therapy be defined. Whereas SARS-CoV-2 may follow the epidemiological pattern of SARS-CoV and extinguish slowly over time, there is yet concern that SARS-CoV-2 may establish itself as an endemic human respiratory coronavirus similar to OC43, 2299E, NL63, and HKU1. Until sufficient data are acquired to better understand the potential of SARS-CoV-2, continued work on antiviral therapy and vaccination is imperative.
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Affiliation(s)
- Nevio Cimolai
- Nevio Cimolai, MD, FRCPC, is a Professor, Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia; he is also Medical Staff, Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia; both in Vancouver, Canada
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Burimuah V, Sylverken A, Owusu M, El-Duah P, Yeboah R, Lamptey J, Frimpong YO, Agbenyega O, Folitse R, Emikpe B, Tasiame W, Owiredu EW, Oppong S, Antwi C, Adu-Sarkodie Y, Drosten C. Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana. BMC Vet Res 2020; 16:405. [PMID: 33109183 PMCID: PMC7590242 DOI: 10.1186/s12917-020-02606-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/01/2020] [Indexed: 11/28/2022] Open
Abstract
Background Apart from the huge worldwide economic losses often occasioned by bovine coronavirus (BCoV) to the livestock industry, particularly with respect to cattle rearing, continuous surveillance of the virus in cattle and small ruminants is essential in monitoring variations in the virus that could enhance host switching. In this study, we collected rectal swabs from a total of 1,498 cattle, sheep and goats. BCoV detection was based on reverse transcriptase polymerase chain reaction. Sanger sequencing of the partial RNA-dependent RNA polymerase (RdRp) region for postive samples were done and nucleotide sequences were compared with homologous sequences from the GenBank. Results The study reports a BCoV prevalence of 0.3%, consisting of 4 positive cases; 3 goats and 1 cattle. Less than 10% of all the animals sampled showed clinical signs such as diarrhea and respiratory distress except for high temperature which occurred in > 1000 of the animals. However, none of the 4 BCoV positive animals manifested any clinical signs of the infection at the time of sample collection. Bayesian majority-rule cladogram comparing partial and full length BCoV RdRp genes obtained in the study to data from the GenBank revealed that the sequences obtained from this study formed one large monophyletic group with those from different species and countries. The goat sequences were similar to each other and clustered within the same clade. No major variations were thus observed between our isolates and those from elsewhere. Conclusions Given that Ghana predominantly practices the extensive and semi-intensive systems of animal rearing, our study highlights the potential for spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species.
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Affiliation(s)
- Vitus Burimuah
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana. .,School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana. .,Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana.
| | - Augustina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana.,Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana.,Department of Medical Laboratory Technology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Philip El-Duah
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana.,Institute of Virology, Universitätsmedizin Berlin, Charite, Germany
| | - Richmond Yeboah
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Jones Lamptey
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Yaw Oppong Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana.,Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Olivia Agbenyega
- Department of Agroforestry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Raphael Folitse
- School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ben Emikpe
- School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - William Tasiame
- School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Institute of Virology, Universitätsmedizin Berlin, Charite, Germany
| | - Eddie-Williams Owiredu
- Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel Oppong
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Christopher Antwi
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Prabhakar PK, Lakhanpal J. Recent advances in the nucleic acid-based diagnostic tool for coronavirus. Mol Biol Rep 2020; 47:9033-9041. [PMID: 33025503 PMCID: PMC7538041 DOI: 10.1007/s11033-020-05889-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/30/2020] [Indexed: 12/15/2022]
Abstract
Abstract Recently in China, a novel coronavirus outbreak took place which caused pneumonia-like symptoms. This coronavirus belongs to the family of SARS and MERS and causes respiratory system disease known as COVID-19. At present we use polymerase chain reaction (PCR) based molecular biology methods for the detection of coronavirus. Other than these PCR based methods, some improved methods also exist such as microarray-based techniques, Real time-quantitative PCR, CRISPR-Cas13 based tools but almost all of the available methods have advantages and disadvantages. There are many limitations associated with this method and hence there is a need for a fast, more sensitive, and specific diagnostic tool which can detect a greater number of samples in less time. Here we have summarised currently available nucleic acid-based diagnostic methods for the detection of coronavirus and the need for developing a better technique for a fast and sensitive detection of coronavirus infections. Graphic abstract
Nucleic acid based detection tool for SARS-CoV-2.![]()
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Affiliation(s)
- Pranav Kumar Prabhakar
- Department of Medical Laboratory Sciences, Lovely Professional University, Punjab, 144411, India.
| | - Jyoti Lakhanpal
- Department of Medical Laboratory Sciences, Lovely Professional University, Punjab, 144411, India
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Hanpanich O, Saito K, Shimada N, Maruyama A. One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer. Biosens Bioelectron 2020; 165:112383. [PMID: 32729508 PMCID: PMC7836245 DOI: 10.1016/j.bios.2020.112383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
RNA detection permits early diagnosis of several infectious diseases and cancers, which prevent propagation of diseases and improve treatment efficacy. However, standard technique for RNA detection such as reverse transcription-quantitative polymerase chain reaction has complicated procedure and requires well-trained personnel and specialized lab equipment. These shortcomings limit the application for point-of-care analysis which is critical for rapid and effective disease management. The multicomponent nucleic acid enzymes (MNAzymes) are one of the promising biosensors for simple, isothermal and enzyme-free RNA detection. Herein, we demonstrate simple yet effective strategies that significantly enhance analytical performance of MNAzymes. The addition of the cationic copolymer and structural modification of MNAzyme significantly enhanced selectivity and activity of MNAzymes by 250 fold and 2,700 fold, respectively. The highly simplified RNA detection system achieved a detection limit of 73 fM target concentration without additional amplification. The robustness of MNAzyme in the presence of non-target RNA was also improved. Our finding opens up a route toward the development of an alternative rapid, sensitive, isothermal, and protein-free RNA diagnostic tool, which expected to be of great clinical significance.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ken Saito
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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Balakrishnan V, Lakshminarayanan K. Screening of FDA Approved Drugs Against SARS-CoV-2 Main Protease: Coronavirus Disease. Int J Pept Res Ther 2020; 27:651-658. [PMID: 33013255 PMCID: PMC7521772 DOI: 10.1007/s10989-020-10115-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 12/04/2022]
Abstract
At the end of December 2019, a new strain of coronavirus was identified in the Wuhan city of Hubei province in China. Within a shorter period of time, an unprecedented outbreak of this strain was witnessed over the entire Wuhan city. This novel coronavirus strain was later officially renamed as COVID-19 (Coronavirus disease 2019) by the World Health Organization. The mode of transmission was human-to-human contact and hence resulted in a rapid surge across the globe where more than 24 million people have been infected with COVID-19. In the current scenario, finding potent drug candidates for the treatment of COVID-19 has emerged as the most challenging task for clinicians and researchers worldwide. Identification of new drugs and vaccine development may take from a few months to years based on the clinical trial processes. To overcome the several limitations involved in identifying and bringing out potent drug candidates for treating COVID-19, in the present study attempts were made to screen the FDA approved drugs using High Throughput Virtual Screening (HTVS). The COVID-19 main protease (COVID-19 Mpro) was chosen as the drug target for which the FDA approved drugs were initially screened with HTVS. The drug candidates that exhibited favorable docking score, energy, and emodel calculations were further taken for performing Induced Fit Docking (IFD) using Schrodinger’s GLIDE. From the flexible docking results, the following four FDA approved drugs Sincalide, Pentagastrin, Ritonavir, and Phytonadione were identified. In particular, Sincalide and Pentagastrin can be considered potential key players for the treatment of COVID-19 disease.
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Affiliation(s)
- Vijayakumar Balakrishnan
- São Carlos Institute of Physics (IFSC), University of São Paulo, Av. Joao Dagnone, 1100 – Jardim Santa Angelina, São Carlos, 13563-120 Brazil
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Nickbakhsh S, Ho A, Marques DFP, McMenamin J, Gunson RN, Murcia PR. Epidemiology of Seasonal Coronaviruses: Establishing the Context for the Emergence of Coronavirus Disease 2019. J Infect Dis 2020; 222:17-25. [PMID: 32296837 PMCID: PMC7184404 DOI: 10.1093/infdis/jiaa185] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Public health preparedness for coronavirus (CoV) disease 2019 (COVID-19) is challenging in the absence of setting-specific epidemiological data. Here we describe the epidemiology of seasonal CoVs (sCoVs) and other cocirculating viruses in the West of Scotland, United Kingdom. We analyzed routine diagnostic data for >70 000 episodes of respiratory illness tested molecularly for multiple respiratory viruses between 2005 and 2017. Statistical associations with patient age and sex differed between CoV-229E, CoV-OC43, and CoV-NL63. Furthermore, the timing and magnitude of sCoV outbreaks did not occur concurrently, and coinfections were not reported. With respect to other cocirculating respiratory viruses, we found evidence of positive, rather than negative, interactions with sCoVs. These findings highlight the importance of considering cocirculating viruses in the differential diagnosis of COVID-19. Further work is needed to establish the occurrence/degree of cross-protective immunity conferred across sCoVs and with COVID-19, as well as the role of viral coinfection in COVID-19 disease severity.
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Affiliation(s)
- Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Diogo F P Marques
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Jim McMenamin
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Li D, Zhang J, Li J. Primer design for quantitative real-time PCR for the emerging Coronavirus SARS-CoV-2. Theranostics 2020; 10:7150-7162. [PMID: 32641984 PMCID: PMC7330846 DOI: 10.7150/thno.47649] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/20/2020] [Indexed: 12/28/2022] Open
Abstract
In December 2019, a new coronavirus disease (COVID-19) outbreak occurred in Wuhan, China. Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which is the seventh coronavirus known to infect humans, is highly contagious and has rapidly expanded worldwide since its discovery. Quantitative nucleic acid testing has become the gold standard for diagnosis and guiding clinical decisions regarding the use of antiviral therapy. However, the RT-qPCR assays targeting SARS-CoV-2 have a number of challenges, especially in terms of primer design. Primers are the pivotal components of a RT-qPCR assay. Once virus mutation and recombination occur, it is difficult to effectively diagnose viral infection by existing RT-qPCR primers. Some primers and probes have also been made available on the WHO website for reference. However, no previous review has systematically compared the previously reported primers and probes and described how to design new primers in the event of a new coronavirus infection. This review focuses on how primers and probes can be designed methodically and rationally, and how the sensitivity and specificity of the detection process can be improved. This brief review will be useful for the accurate diagnosis and timely treatment of the new coronavirus pneumonia.
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Coronavirus Infections in Children Including COVID-19: An Overview of the Epidemiology, Clinical Features, Diagnosis, Treatment and Prevention Options in Children. Pediatr Infect Dis J 2020. [PMID: 32310621 DOI: 10.1097/inf.0000000000002660)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coronaviruses (CoVs) are a large family of enveloped, single-stranded, zoonotic RNA viruses. Four CoVs commonly circulate among humans: HCoV2-229E, -HKU1, -NL63 and -OC43. However, CoVs can rapidly mutate and recombine leading to novel CoVs that can spread from animals to humans. The novel CoVs severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012. The 2019 novel coronavirus (SARS-CoV-2) is currently causing a severe outbreak of disease (termed COVID-19) in China and multiple other countries, threatening to cause a global pandemic. In humans, CoVs mostly cause respiratory and gastrointestinal symptoms. Clinical manifestations range from a common cold to more severe disease such as bronchitis, pneumonia, severe acute respiratory distress syndrome, multi-organ failure and even death. SARS-CoV, MERS-CoV and SARS-CoV-2 seem to less commonly affect children and to cause fewer symptoms and less severe disease in this age group compared with adults, and are associated with much lower case-fatality rates. Preliminary evidence suggests children are just as likely as adults to become infected with SARS-CoV-2 but are less likely to be symptomatic or develop severe symptoms. However, the importance of children in transmitting the virus remains uncertain. Children more often have gastrointestinal symptoms compared with adults. Most children with SARS-CoV present with fever, but this is not the case for the other novel CoVs. Many children affected by MERS-CoV are asymptomatic. The majority of children infected by novel CoVs have a documented household contact, often showing symptoms before them. In contrast, adults more often have a nosocomial exposure. In this review, we summarize epidemiologic, clinical and diagnostic findings, as well as treatment and prevention options for common circulating and novel CoVs infections in humans with a focus on infections in children.
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Zimmermann P, Curtis N. Coronavirus Infections in Children Including COVID-19: An Overview of the Epidemiology, Clinical Features, Diagnosis, Treatment and Prevention Options in Children. Pediatr Infect Dis J 2020; 39:355-368. [PMID: 32310621 PMCID: PMC7158880 DOI: 10.1097/inf.0000000000002660] [Citation(s) in RCA: 671] [Impact Index Per Article: 167.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
Coronaviruses (CoVs) are a large family of enveloped, single-stranded, zoonotic RNA viruses. Four CoVs commonly circulate among humans: HCoV2-229E, -HKU1, -NL63 and -OC43. However, CoVs can rapidly mutate and recombine leading to novel CoVs that can spread from animals to humans. The novel CoVs severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012. The 2019 novel coronavirus (SARS-CoV-2) is currently causing a severe outbreak of disease (termed COVID-19) in China and multiple other countries, threatening to cause a global pandemic. In humans, CoVs mostly cause respiratory and gastrointestinal symptoms. Clinical manifestations range from a common cold to more severe disease such as bronchitis, pneumonia, severe acute respiratory distress syndrome, multi-organ failure and even death. SARS-CoV, MERS-CoV and SARS-CoV-2 seem to less commonly affect children and to cause fewer symptoms and less severe disease in this age group compared with adults, and are associated with much lower case-fatality rates. Preliminary evidence suggests children are just as likely as adults to become infected with SARS-CoV-2 but are less likely to be symptomatic or develop severe symptoms. However, the importance of children in transmitting the virus remains uncertain. Children more often have gastrointestinal symptoms compared with adults. Most children with SARS-CoV present with fever, but this is not the case for the other novel CoVs. Many children affected by MERS-CoV are asymptomatic. The majority of children infected by novel CoVs have a documented household contact, often showing symptoms before them. In contrast, adults more often have a nosocomial exposure. In this review, we summarize epidemiologic, clinical and diagnostic findings, as well as treatment and prevention options for common circulating and novel CoVs infections in humans with a focus on infections in children.
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Affiliation(s)
- Petra Zimmermann
- From the Department of Paediatrics, Fribourg Hospital HFR and Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, The University of Melbourne
- Infectious Diseases Research Group, Murdoch Children’s Research Institute
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne
- Infectious Diseases Research Group, Murdoch Children’s Research Institute
- Infectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
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Shen M, Zhou Y, Ye J, Abdullah Al-Maskri AA, Kang Y, Zeng S, Cai S. Recent advances and perspectives of nucleic acid detection for coronavirus. J Pharm Anal 2020; 10:97-101. [PMID: 32292623 PMCID: PMC7102540 DOI: 10.1016/j.jpha.2020.02.010] [Citation(s) in RCA: 285] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
The recent pneumonia outbreak caused by a novel coronavirus (SARS-CoV-2) is posing a great threat to global public health. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people’s lives and preventing epidemics. It is important to establish a quick standard diagnostic test for the detection of the infectious disease (COVID-19) to prevent subsequent secondary spread. Polymerase chain reaction (PCR) is regarded as a gold standard test for the molecular diagnosis of viral and bacterial infections with high sensitivity and specificity. Isothermal nucleic acid amplification is considered to be a highly promising candidate method due to its fundamental advantage in quick procedure time at constant temperature without thermocycler operation. A variety of improved or new approaches also have been developed. This review summarizes the currently available detection methods for coronavirus nucleic acid. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection. This review summarizes the currently available detection methods for coronavirus nucleic acid. It will assist researchers in developing better techniques for timely and effective detection of coronavirus infection. It will help the establishment of SARS-CoV-2 RNA detection method which is useful for the early diagnosis of COVID-19.
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Affiliation(s)
- Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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Plotkin SA. The New Coronavirus, the Current King of China. J Pediatric Infect Dis Soc 2020; 9:1-2. [PMID: 32083284 PMCID: PMC7107562 DOI: 10.1093/jpids/piaa018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 11/13/2022]
Affiliation(s)
- Stanley A Plotkin
- Emeritus Professor of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Vaxconsult, Doylestown, Pennsylvania, USA,Correspondence: Stanley A. Plotkin, Vaxconsult, 4650 Wismer Rd, Doylestown, PA 18902. E-mail:
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Yamaya M, Nishimura H, Deng X, Sugawara M, Watanabe O, Nomura K, Shimotai Y, Momma H, Ichinose M, Kawase T. Inhibitory effects of glycopyrronium, formoterol, and budesonide on coronavirus HCoV-229E replication and cytokine production by primary cultures of human nasal and tracheal epithelial cells. Respir Investig 2020; 58:155-168. [PMID: 32094077 PMCID: PMC7102607 DOI: 10.1016/j.resinv.2019.12.005] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/12/2019] [Accepted: 12/26/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Coronavirus 229E (HCoV-229E), one of the causes of the common cold, exacerbates chronic obstructive pulmonary disease (COPD) and bronchial asthma. Long-acting muscarinic antagonists and β2-agonists and inhaled corticosteroids inhibit the exacerbation of COPD and bronchial asthma caused by infection with viruses, including HCoV-229E. However, the effects of these drugs on HCoV-229E replication and infection-induced inflammation in the human airway are unknown. METHODS Primary human nasal (HNE) and tracheal (HTE) epithelial cell cultures were infected with HCoV-229E. RESULTS Pretreatment of HNE and HTE cells with glycopyrronium or formoterol decreased viral RNA levels and/or titers, the expression of the HCoV-229E receptor CD13, the number and fluorescence intensity of acidic endosomes where HCoV-229E RNA enters the cytoplasm, and the infection-induced production of cytokines, including IL-6, IL-8, and IFN-β. Treatment of the cells with the CD13 inhibitor 2'2'-dipyridyl decreased viral titers. Pretreatment of the cells with a combination of three drugs (glycopyrronium, formoterol, and budesonide) exerted additive inhibitory effects on viral titers and cytokine production. Pretreatment of HNE cells with glycopyrronium or formoterol reduced the susceptibility to infection, and pretreatment with the three drugs inhibited activation of nuclear factor-kappa B p50 and p65 proteins. Pretreatment with formoterol increased cAMP levels and treatment with cAMP decreased viral titers, CD13 expression, and the fluorescence intensity of acidic endosomes. CONCLUSIONS These findings suggest that glycopyrronium, formoterol, and a combination of glycopyrronium, formoterol, and budesonide inhibit HCoV-229E replication partly by inhibiting receptor expression and/or endosomal function and that these drugs modulate infection-induced inflammation in the airway.
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Affiliation(s)
- Mutsuo Yamaya
- Department of Advanced Preventive Medicine for Infectious Disease, Tohoku University School of Medicine, Sendai, Japan.
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai, Japan.
| | - Xue Deng
- Department of Advanced Preventive Medicine for Infectious Disease, Tohoku University School of Medicine, Sendai, Japan.
| | - Mitsuru Sugawara
- Department of Otolaryngology, Tohoku Kosai Hospital, Sendai, Japan.
| | - Oshi Watanabe
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai, Japan.
| | - Kazuhiro Nomura
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Yoshitaka Shimotai
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan.
| | - Haruki Momma
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Masakazu Ichinose
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Tetsuaki Kawase
- Laboratory of Rehabilitative Auditory Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.
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Xie C, Lau EHY, Yoshida T, Yu H, Wang X, Wu H, Wei J, Cowling B, Peiris M, Li Y, Yen HL. Detection of Influenza and Other Respiratory Viruses in Air Sampled From a University Campus: A Longitudinal Study. Clin Infect Dis 2020; 70:850-858. [PMID: 30963180 PMCID: PMC7108140 DOI: 10.1093/cid/ciz296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/04/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Respiratory virus-laden particles are commonly detected in the exhaled breath of symptomatic patients or in air sampled from healthcare settings. However, the temporal relationship of detecting virus-laden particles at nonhealthcare locations vs surveillance data obtained by conventional means has not been fully assessed. METHODS From October 2016 to June 2018, air was sampled weekly from a university campus in Hong Kong. Viral genomes were detected and quantified by real-time reverse-transcription polymerase chain reaction. Logistic regression models were fitted to examine the adjusted odds ratios (aORs) of ecological and environmental factors associated with the detection of virus-laden airborne particles. RESULTS Influenza A (16.9% [117/694]) and influenza B (4.5% [31/694]) viruses were detected at higher frequencies in air than rhinovirus (2.2% [6/270]), respiratory syncytial virus (0.4% [1/270]), or human coronaviruses (0% [0/270]). Multivariate analyses showed that increased crowdedness (aOR, 2.3 [95% confidence interval {CI}, 1.5-3.8]; P < .001) and higher indoor temperature (aOR, 1.2 [95% CI, 1.1-1.3]; P < .001) were associated with detection of influenza airborne particles, but absolute humidity was not (aOR, 0.9 [95% CI, .7-1.1]; P = .213). Higher copies of influenza viral genome were detected from airborne particles >4 μm in spring and <1 μm in autumn. Influenza A(H3N2) and influenza B viruses that caused epidemics during the study period were detected in air prior to observing increased influenza activities in the community. CONCLUSIONS Air sampling as a surveillance tool for monitoring influenza activity at public locations may provide early detection signals on influenza viruses that circulate in the community.
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Affiliation(s)
- Chenyi Xie
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tomoyo Yoshida
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Han Yu
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xin Wang
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Huitao Wu
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jianjian Wei
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ben Cowling
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yuguo Li
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
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A. Desheva Y, S. Mamontov A, G. Nazarov P. Contribution of antibody-dependent enhancement to the pathogenesis of coronavirus infections. AIMS ALLERGY AND IMMUNOLOGY 2020. [DOI: 10.3934/allergy.2020005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Abstract
Hintergrund Es gibt sechs humanpathogene Coronaviren (CoV), die vornehmlich respiratorische Infektionen auslösen. Im klinischen Alltag ist es hilfreich, Relevanz und Besonderheiten dieser Erreger zu kennen. Fragestellung Praxisnahe Darstellung der Epidemiologie, Klinik und Unterschiede humanpathogener CoV. Hinweise zu Diagnostik und Umgang mit Patienten bei Verdacht auf eine CoV-Infektion. Material und Methoden Selektive Literaturrecherche, Darstellung und Diskussion von Grundlagenarbeiten und Expertenempfehlungen einschließlich der Veröffentlichungen der Weltgesundheitsorganisation (WHO), des Europäischen Zentrums für die Prävention und die Kontrolle von Krankheiten (ECDC) und des Robert Koch-Instituts. Ergebnisse Die weltweit endemischen CoV (HCoV-NL63, -229E, -OC43 und -HKU1) sind häufige Ursache von leichteren respiratorischen Infektionen. Zwei epidemische, zoonotische Coronaviren (SARS- und MERS-CoV, MERS „Middle East respiratory syndrome“, SARS „severe acute respiratory syndrome“ [schweres akutes Atemwegssyndrom]) können schwere Pneumonien hervorrufen. SARS-CoV ist seit 15 Jahren nicht mehr im Menschen nachgewiesen worden. MERS-CoV zirkuliert seit 2012 hauptsächlich auf der Arabischen Halbinsel. Eine spezifische Therapie oder zugelassene Impfung existiert noch für keines der sechs humanpathogenen Coronaviren. Schlussfolgerung Eine Erregerdiagnostik mittels Polymerase-Kettenreaktion aus respiratorischem Material ist für alle CoV möglich, für die vier endemischen allerdings selten notwendig. SARS-CoV hat aktuell keine Relevanz in der Klinik, da es seit 15 Jahren nicht mehr im Menschen nachgewiesen wurde. Der Verdacht auf eine MERS-Infektion sollte hingegen bei entsprechender Symptomatik und Reiseanamnese differenzialdiagnostisch in Betracht gezogen werden. Hier sind eine schnelle Diagnosesicherung und allgemeine Hygienemaßnahmen zur Verhinderung der Verbreitung entscheidend.
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Affiliation(s)
- V M Corman
- Institut für Virologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Deutschland
| | - J Lienau
- Arbeitsbereich Pulmonale Inflammation, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Deutschland
| | - M Witzenrath
- Arbeitsbereich Pulmonale Inflammation, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Deutschland. .,Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Deutschland.
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Abe N, Yasudo H, Fukano R, Nakamura T, Okada S, Wakiguchi H, Okazaki F, Shirabe K, Toda S, Okamoto R, Ouchi K, Ohga S, Hasegawa S. Multi-season analyses of causative pathogens in children hospitalized with asthma exacerbation. Pediatr Allergy Immunol 2019; 30:724-731. [PMID: 31251831 PMCID: PMC7167852 DOI: 10.1111/pai.13102] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Respiratory viral and mycoplasma infections are associated with childhood asthma exacerbations. Here, we explored epidemiologic profile of causative pathogens and possible factors for exacerbation in a single center over a three-year period. METHODS Hospitalized asthmatic children with attack aged 6 months-17 years were recruited between 2012 and 2015 (n = 216). Nasopharyngeal mucosa cell samples were collected from the participants and examined by reverse transcription-polymerase chain reaction to detect rhinovirus (RV), respiratory syncytial virus (RSV), enterovirus (EV), parainfluenza virus (PIV), Mycoplasma pneumoniae, and others. Clinical features, laboratory data, asthma exacerbation intensity, and asthma severity were compared among participants. Epidemiologic profile of causative pathogens and possible factors for exacerbation were explored. RESULTS Viruses and/or Mycoplasma pneumoniae were detected in 75% of the participants. Rhinovirus (48%) was the most commonly detected virus in the participants with single infection, followed by RSV (6%). The median age at admission in the RV group was significantly higher than that in the RSV group. Insufficient asthma control and allergen sensitization were significantly related to RV-associated asthma exacerbation. There was no seasonality of pathogen types associated with asthma exacerbation although a sporadic prevalence of EV-D68 was observehinovirud. Rhinovirus were repeatedly detected in multiple admission cases. CONCLUSION Our three-year analysis revealed that patients with RV infection were significantly prone to repeated RV infection in the subsequent exacerbation and good asthma control could prevent RV-associated asthma development and exacerbation. Multiple-year monitoring allowed us to comprehend the profile of virus- and/or mycoplasma-induced asthma exacerbation.
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Affiliation(s)
- Nozomi Abe
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroki Yasudo
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Reiji Fukano
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Tamaki Nakamura
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Seigo Okada
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroyuki Wakiguchi
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Fumiko Okazaki
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Shoichi Toda
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Reiko Okamoto
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Kazunobu Ouchi
- Department of Pediatrics, Kawasaki Medical School, Kurashiki, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shunji Hasegawa
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
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49
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de Steenhuijsen Piters WAA, Jochems SP, Mitsi E, Rylance J, Pojar S, Nikolaou E, German EL, Holloway M, Carniel BF, Chu MLJN, Arp K, Sanders EAM, Ferreira DM, Bogaert D. Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine. Nat Commun 2019; 10:2981. [PMID: 31278315 PMCID: PMC6611866 DOI: 10.1038/s41467-019-10814-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is the main bacterial pathogen involved in pneumonia. Pneumococcal acquisition and colonization density is probably affected by viral co-infections, the local microbiome composition and mucosal immunity. Here, we report the interactions between live-attenuated influenza vaccine (LAIV), successive pneumococcal challenge, and the healthy adult nasal microbiota and mucosal immunity using an experimental human challenge model. Nasal microbiota profiles at baseline are associated with consecutive pneumococcal carriage outcome (non-carrier, low-dense and high-dense pneumococcal carriage), independent of LAIV co-administration. Corynebacterium/Dolosigranulum-dominated profiles are associated with low-density colonization. Lowest rates of natural viral co-infection at baseline and post-LAIV influenza replication are detected in the low-density carriers. Also, we detected the fewest microbiota perturbations and mucosal cytokine responses in the low-density carriers compared to non-carriers or high-density carriers. These results indicate that the complete respiratory ecosystem affects pneumococcal behaviour following challenge, with low-density carriage representing the most stable ecological state.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Simon P Jochems
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Esther L German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mark Holloway
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Beatriz F Carniel
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands.
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom.
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50
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Kockuzu E, Bayrakcı B, Kesici S, Cıtak A, Karapınar B, Emeksiz S, Anıl AB, Kendirli T, Yukselmis U, Sevketoglu E, Paksu Ş, Kutlu O, Agın H, Yıldızdas D, Keskin H, Kalkan G, Hasanoglu A, Yazıcı MU, Sık G, Kılınc A, Durak F, Perk O, Talip M, Yener N, Uzuner S. Comprehensive Analysis of Severe Viral Infections of Respiratory Tract admitted to PICUs during the Winter Season in Turkey. Indian J Crit Care Med 2019; 23:263-269. [PMID: 31435144 PMCID: PMC6698354 DOI: 10.5005/jp-journals-10071-23177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in pediatric intensive care units (PICU) of 16 centers in Turkey. MATERIALS AND METHODS It is a retrospective, observational, and multicenter study conducted in 16 tertiary PICUs in Turkey includes a total of 302 children with viral cause in the nasal swab which required PICU admission with no interventions. RESULTS Median age of patients was 12 months. Respiratory syncytial virus (RSV) was more common in patients over one year of age whereas influenza, human Bocavirus in patients above a year of age was more common (p <0.05). Clinical presentations influencing mortality were neurologic symptoms, tachycardia, hypoxia, hypotension, elevated lactate, and acidosis. The critical pH value related with mortality was ≤7.10, and critical PCO2 ≥60 mm Hg. CONCLUSION Our findings demonstrate that patients with neurological symptoms, tachycardia, hypoxia, hypotension, acidosis, impaired liver, and renal function at the time of admission exhibit more severe mortal progressions. Presence of acidosis and multiorgan failure was found to be predictor for mortality. Knowledge of clinical presentation and age-related variations among seasonal viruses may give a clue about severe course and prognosis. By presenting the analyzed data of 302 PICU admissions, current study reveals severity of viral respiratory tract infections and release tips for handling them. HOW TO CITE THIS ARTICLE Kockuzu E, Bayrakcı B, Kesici S, Cıtak A, Karapınar K, Emeksiz S, et al. Comprehensive Analysis of Severe Viral Infections of Respiratory Tract admitted to PICUs During the Winter Season in Turkey. Indian J Crit Care Med 2019;23(6):263-269.
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Affiliation(s)
- Esra Kockuzu
- Department of Pediatric Intensive Care Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Benan Bayrakcı
- Department of Pediatric Intensive Care Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Selman Kesici
- Clinic of Pediatric Intensive Care Unit, Dr. Sami Ulus Child Health and Disease Training and Research Hospital, Ankara, Turkey
| | - Agop Cıtak
- Department of Pediatric Intensive Care Unit, Acıbadem University Faculty of Medicine, Istanbul, Turkey
| | - Bulent Karapınar
- Department of Pediatric Intensive Care Unit, Ege University Faculty of Medicine, Izmir, Turkey
| | - Serhat Emeksiz
- Clinic of Pediatric Intensive Care Unit, Ankara Pediatric Hematology Oncology Training and Research Hospital, Ankara, Turkey
| | - Ayşe Berna Anıl
- Clinic of Pediatric Intensive Care Unit, Ankara Tepecik Training and Research Hospital, Izmir, Turkey
| | - Tanıl Kendirli
- Department of Pediatric Intensive Care Unit, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Ufuk Yukselmis
- Clinic of Pediatric Intensive Care Unit, Kartal Lutfi Kırdar Education Research Hospital, Istanbul, Turkey
| | - Esra Sevketoglu
- Clinic of Pediatric Intensive Care Unit, Bakırkoy Sadi Konuk Education Research Hospital, Istanbul, Turkey
| | - Şukru Paksu
- Department of Pediatric Intensive Care Unit, Ondokuz Mayıs University, Faculty of Medicine, Samsun, Turkey
| | - Onur Kutlu
- Department of Pediatric Intensive Care Unit, Bezmialem University Faculty of Medicine, Istanbul, Turkey
| | - Hasan Agın
- Clinic of Pediatric Intensive Care Unit Dr. Behcet Uz Education Research Hospital, Izmir, Turkey
| | - Dincer Yıldızdas
- Department of Pediatric Intensive Care Unit, Cukurova University Faculty of Medicine, Adana, Turkey
| | - Halil Keskin
- Department of Pediatric Intensive Care Unit, Ataturk University Faculty of Medicine, Erzurum, Turkey
| | - Gokhan Kalkan
- Department of Pediatric Intensive Care Unit, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Arzu Hasanoglu
- Department of Pediatric Intensive Care Unit, Gaziantep University Faculty of Medicine, Gaziantep, Turkey
| | - Mutlu Uysal Yazıcı
- Department of Pediatric Intensive Care Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Guntulu Sık
- Clinic of Pediatric Intensive Care Unit, Dr. Sami Ulus Child Health and Disease Training and Research Hospital, Ankara, Turkey
| | - Arda Kılınc
- Department of Pediatric Intensive Care Unit, Ege University Faculty of Medicine, Izmir, Turkey
| | - Fatih Durak
- Department of Pediatric Intensive Care Unit, Ege University Faculty of Medicine, Izmir, Turkey
| | - Oktay Perk
- Department of Pediatric Intensive Care Unit, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Mey Talip
- Clinic of Pediatric Intensive Care Unit, Bakırkoy Sadi Konuk Education Research Hospital, Istanbul, Turkey
| | - Nazik Yener
- Department of Pediatric Intensive Care Unit, Ondokuz Mayıs University, Faculty of Medicine, Samsun, Turkey
| | - Selcuk Uzuner
- Department of Pediatric Intensive Care Unit, Bezmialem University Faculty of Medicine, Istanbul, Turkey
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