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Grizer CS, Messacar K, Mattapallil JJ. Enterovirus-D68 - A Reemerging Non-Polio Enterovirus that Causes Severe Respiratory and Neurological Disease in Children. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2024; 4:1328457. [PMID: 39246649 PMCID: PMC11378966 DOI: 10.3389/fviro.2024.1328457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
The past decade has seen the global reemergence and rapid spread of enterovirus D68 (EV-D68), a respiratory pathogen that causes severe respiratory illness and paralysis in children. EV-D68 was first isolated in 1962 from children with pneumonia. Sporadic cases and small outbreaks have been reported since then with a major respiratory disease outbreak in 2014 associated with an increased number of children diagnosed with polio-like paralysis. From 2014-2018, major outbreaks have been reported every other year in a biennial pattern with > 90% of the cases occurring in children under the age of 16. With the outbreak of SARS-CoV-2 and the subsequent COVID-19 pandemic, there was a significant decrease in the prevalence EV-D68 cases along with other respiratory diseases. However, since the relaxation of pandemic social distancing protocols and masking mandates the number of EV-D68 cases have begun to rise again - culminating in another outbreak in 2022. Here we review the virology, pathogenesis, and the immune response to EV-D68, and discuss the epidemiology of EV-D68 infections and the divergence of contemporary strains from historical strains. Finally, we highlight some of the key challenges in the field that remain to be addressed.
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Affiliation(s)
- Cassandra S Grizer
- Department of Microbiology & Immunology, The Henry M. Jackson Foundation for Military Medicine, Uniformed Services University, Bethesda, MD 20814, USA
| | - Kevin Messacar
- The Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Joseph J Mattapallil
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
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Han Z, Wang F, Xiao J, Fu H, Song Y, Jiang M, Lu H, Li J, Xu Y, Zhu R, Zhang Y, Zhao L. Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts. Virus Evol 2023; 10:vead080. [PMID: 38361814 PMCID: PMC10868544 DOI: 10.1093/ve/vead080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/05/2023] [Accepted: 12/17/2023] [Indexed: 02/17/2024] Open
Abstract
Coxsackievirus A16 (CVA16) is a major pathogen that causes hand, foot, and mouth disease (HFMD). The recombination form (RF) shifts and global transmission dynamics of CVA16 remain unknown. In this retrospective study, global sequences of CVA16 were retrieved from the GenBank database and analyzed using comprehensive phylogenetic inference, RF surveys, and population structure. A total of 1,663 sequences were collected, forming a 442-sequences dataset for VP1 coding region analysis and a 345-sequences dataset for RF identification. Based on the VP1 coding region used for serotyping, three genotypes (A, B, and D), two subgenotypes of genotype B (B1 and B2), and three clusters of subgenotype B1 (B1a, B1b, and B1c) were identified. Cluster B1b has dominated the global epidemics, B2 disappeared in 2000, and D is an emerging genotype dating back to August 2002. Globally, four oscillation phases of CVA16 evolution, with a peak in 2013, and three migration pathways were identified. Europe, China, and Japan have served as the seeds for the global transmission of CVA16. Based on the 3D coding region of the RFs, five clusters of RFs (RF-A to -E) were identified. The shift in RFs from RF-B and RF-C to RF-D was accompanied by a change in genotype from B2 to B1a and B1c and then to B1b. In conclusion, the evolution and population dynamics of CVA16, especially the coevolution of 3D and VP1 genes, revealed that genotype evolution and RF replacement were synergistic rather than stochastic.
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Affiliation(s)
| | - Fangming Wang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Hanhaoyu Fu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Mingli Jiang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Jichen Li
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Yanpeng Xu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Runan Zhu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Linqing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
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Andino R, Kirkegaard K, Macadam A, Racaniello VR, Rosenfeld AB. The Picornaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens. J Infect Dis 2023; 228:S427-S445. [PMID: 37849401 DOI: 10.1093/infdis/jiac426] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
Picornaviruses are nonenveloped particles with a single-stranded RNA genome of positive polarity. This virus family includes poliovirus, hepatitis A virus, rhinoviruses, and Coxsackieviruses. Picornaviruses are common human pathogens, and infection can result in a spectrum of serious illnesses, including acute flaccid myelitis, severe respiratory complications, and hand-foot-mouth disease. Despite research on poliovirus establishing many fundamental principles of RNA virus biology and the first transgenic animal model of disease for infection by a human virus, picornaviruses are understudied. Existing knowledge gaps include, identification of molecules required for virus entry, understanding cellular and humoral immune responses elicited during virus infection, and establishment of immune-competent animal models of virus pathogenesis. Such knowledge is necessary for development of pan-picornavirus countermeasures. Defining enterovirus A71 and D68, human rhinovirus C, and echoviruses 29 as prototype pathogens of this virus family may provide insight into picornavirus biology needed to establish public health strategies necessary for pandemic preparedness.
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Affiliation(s)
- Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Karla Kirkegaard
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, California, USA
| | - Andrew Macadam
- National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom
| | - Vincent R Racaniello
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Amy B Rosenfeld
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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Wolf J. Insights into the molecular evolution of enterovirus D68. Arch Virol 2023; 168:268. [PMID: 37804367 DOI: 10.1007/s00705-023-05894-4] [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: 06/21/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023]
Abstract
Enterovirus D68 (EV-D68) is a respiratory virus that primarily affects children and has been associated with sporadic outbreaks of respiratory illness worldwide. In the present study, temporal spreading and molecular evolution of EV-D68 clades (A1, A2, B, B1, B2, B3, and C) were evaluated. Bayesian coalescent analysis was performed to study viral evolution. Data from 976 whole-genome sequences (WGSs) collected between 1977 and 2022 were evaluated. For A1, the most recent common ancestor was dated to 2005-04-17 in the USA; for A2 it was 2003-12-23 in China; for B, it was 2003-07-06 in China; for B1, it was 2010-03-21 in Vietnam; for B2, it was 2006-11-25 in Vietnam; for B3, it was 2011-01-15 in China; and for C, it was 2000-06-27 in the USA. The molecular origin of EV-D68 was in Canada in 1995, and later it was disseminated in France in 1997, the USA in 1999, Asia in 2008, the Netherlands in 2009, New Zealand in 2010, Mexico in 2014, Kenya in 2015, Sweden in 2016, Switzerland in 2018, Spain in 2018, Belgium in 2018, Australia in 2018, and Denmark in 2019. In 2022, this virus circulated in the USA. In conclusion, EV-D68 originated in Canada in the 1990s and spread to Europe, Asia, Oceania, Latin America, and Africa.
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Affiliation(s)
- Jonas Wolf
- Clinical practice management office, Medical Manager at Hospital Moinhos de Vento, 333 Tiradentes Street, 13 floor, Porto Alegre, RS, 90560-030, Brazil.
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Shi Y, Ran Q, Wang X, Shi L. Seroprevalence of Enterovirus D68 Infection among Humans: A Systematic Review and Meta-Analysis. Intervirology 2023; 66:111-121. [PMID: 37793363 PMCID: PMC10614446 DOI: 10.1159/000531853] [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: 03/12/2022] [Accepted: 06/26/2023] [Indexed: 10/06/2023] Open
Abstract
INTRODUCTION Human enterovirus D68 (EV-D68), which belongs to enteroviruses of the small RNA family, is a type of enterovirus that can cause acute respiratory tract infection and central nervous system diseases. This study systematically analysed and summarized EV-D68 antibody studies in databases and identified the seropositivity rates of different regions, ages, and sexes. METHODS Meta-analysis was performed using STATA 16.0 software. I2 and Q tests were used to analyse the heterogeneity of the included studies. Meta-regression analysis was performed for different groups, and Egger's linear regression analysis was used to evaluate publication bias. RESULTS The results of multiple studies indicated that the serological prevalence range of EV-D68 antibody was 17.78-96.69%. The results of the meta-analysis showed that the seropositivity rate of EV-D68 antibody was 76% (95% confidence interval [CI]: 67-84%), among which that of the Chinese population was 74% (95% CI: 61-86%) and that of other countries was 79% (95% CI: 65-91%). At the same time, a subgroup analysis was conducted. The seroprevalence of EV-D68 antibody was related to age but not sex or region. CONCLUSION The seropositivity rate was lower in the below 5-year age group; however, it gradually increased with age. The results of this study showed that EV-D68 infection was widespread in the population, and the current clinical infection situation could not reflect the actual epidemic situation of the virus, among which children under 5 years old were vulnerable to infection, which should be given greater attention for epidemic prevention and control.
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Affiliation(s)
- Yingying Shi
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, China
| | - Qinqin Ran
- Department of Nursing, School of Medicine, Jianghan University, Wuhan, China
| | - Xiaochen Wang
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, China
| | - Lu Shi
- Department of Pharmacy, School of Medicine, Jianghan University, Wuhan, China
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Livingston RA, Harrison CJ, Selvarangan R. Neutralizing Enterovirus D68 Antibodies in Children after 2014 Outbreak, Kansas City, Missouri, USA. Emerg Infect Dis 2022; 28:539-547. [PMID: 35201738 PMCID: PMC8888215 DOI: 10.3201/eid2803.211467] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Antibodies to B1, B2, and D clade viruses were detected. Enterovirus D68 (EV-D68) causes severe respiratory illness outbreaks among children, particularly those with asthma. We previously detected neutralizing antibodies against the predominant EV-D68 B1 clade in the 2014 outbreak in serum collected before the outbreak (2012–2013) from persons 24 months to 85 years of age. We recently detected neutralizing antibodies to the 2014 B1, B2, and D clade viruses in serum collected after the 2014 outbreak (April–May 2017) from 300 children 6 months to 18 years of age. B1 virus neutralizing antibodies were found in 100% of patients, even children born after 2014; B2 in 84.6%, and D in 99.6%. In 2017, titers increased with patient age and were higher than titers in 2012–2013 from comparably aged children. Rate of seronegativity was highest (15.3%) for B2 virus. Multivariate analysis revealed an association between asthma and higher titers against B2 and D viruses. EV-D68 seems to have circulated during 2014–2017.
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Rosenfeld AB, Shen EQL, Melendez M, Mishra N, Lipkin WI, Racaniello VR. Cross-Reactive Antibody Responses against Nonpoliovirus Enteroviruses. mBio 2022; 13:e0366021. [PMID: 35038922 PMCID: PMC8764532 DOI: 10.1128/mbio.03660-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/14/2023] Open
Abstract
Enteroviruses are among the most common human viral pathogens. Infection with members of a subgroup of viruses within this genus, the nonpoliovirus enteroviruses (NPEVs), can result in a broad spectrum of serious illnesses, including acute flaccid myelitis (AFM), a polio-like childhood paralysis; neonatal sepsis; aseptic meningitis; myocarditis; and hand-foot-mouth disease. Despite the diverse primary sites of virus infection, including the respiratory and alimentary tracts, and an array of diseases associated with these infections, there is significant genetic and antigenic similarity among NPEVs. This conservation results in the induction of cross-reactive antibodies that are either able to bind and neutralize or bind but not neutralize multiple NPEVs. Using plaque reduction and enzyme-linked immunosorbent assay (ELISA)-based binding assays, we define the antigenic relationship among poliovirus and NPEVs, including multiple isolates of EV-D68, EV-A71, EV-D70, EV-94, EV-111, Coxsackievirus A24v, and rhinovirus. The results reveal extensive cross-reactivity among EVs that cannot be predicted from phylogenetic analysis. Determining the immunologic relationship among EVs is critical to understanding the humoral response elicited during homologous and heterologous virus infections. IMPORTANCE Enteroviruses (EVs) are common human pathogens. Although infection with EVs leads to cross-reactive antibodies, the clinical relevance of these antibodies is unclear given the estimated incidence of EV infections in the general population of one per year. The hypothesis that anti-EV cross-reactive antibodies can bind and neutralize heterologous EVs was investigated using polyclonal sera collected from animals immunized with individual EVs. Both binding and neutralization activities against heterologous EVs was observed in these sera, and we speculate that cross-reactive antibodies may modulate infection and disease severity. Defining the antigenic relationship among EVs may provide insights into the epidemiology and pathogenesis of enterovirus infections.
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Affiliation(s)
- Amy B. Rosenfeld
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Edmund Qian Long Shen
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Michaela Melendez
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Vincent R. Racaniello
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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Rajagopala SV, Bakhoum NG, Pakala SB, Shilts MH, Rosas-Salazar C, Mai A, Boone HH, McHenry R, Yooseph S, Halasa N, Das SR. Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples. CELL REPORTS METHODS 2021; 1:100091. [PMID: 34790908 PMCID: PMC8594859 DOI: 10.1016/j.crmeth.2021.100091] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/18/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022]
Abstract
We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that H. influenzae was highly active in symptomatic RSV subjects. The host nasal transcriptome reveled upregulation of the innate immune system, anti-viral response and inflammasome pathway, and downregulation of fatty acid pathways in children with symptomatic RSV. Overall, we demonstrate that our method is broadly applicable to infer the transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples.
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Affiliation(s)
- Seesandra V. Rajagopala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicole G. Bakhoum
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman B. Pakala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Meghan H. Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christian Rosas-Salazar
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Annie Mai
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Helen H. Boone
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rendie McHenry
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
| | - Natasha Halasa
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Otolaryngology and Head and Neck Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Complete Genome Sequences of Enterovirus D68 Clade A and D Strains in the Philippines. Microbiol Resour Announc 2021; 10:e0070921. [PMID: 34591667 PMCID: PMC8483712 DOI: 10.1128/mra.00709-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Complete genome sequences were determined for 4 clade A and 12 clade D enterovirus D68 strains detected in nasopharyngeal swabs from children with acute respiratory illness in the Philippines. These sequence data will be useful for future epidemiological monitoring, including watching for viral evolution.
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Duval M, Mirand A, Lesens O, Bay JO, Caillaud D, Gallot D, Lautrette A, Montcouquiol S, Schmidt J, Egron C, Jugie G, Bisseux M, Archimbaud C, Lambert C, Henquell C, Bailly JL. Retrospective Study of the Upsurge of Enterovirus D68 Clade D1 among Adults (2014-2018). Viruses 2021; 13:1607. [PMID: 34452471 PMCID: PMC8402803 DOI: 10.3390/v13081607] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/26/2021] [Accepted: 08/08/2021] [Indexed: 11/17/2022] Open
Abstract
Enterovirus D68 (EV-D68) has emerged as an agent of epidemic respiratory illness and acute flaccid myelitis in the paediatric population but data are lacking in adult patients. We performed a 4.5-year single-centre retrospective study of all patients who tested positive for EV-D68 and analysed full-length EV-D68 genomes of the predominant clades B3 and D1. Between 1 June 2014, and 31 December 2018, 73 of the 11,365 patients investigated for respiratory pathogens tested positive for EV-D68, of whom 20 (27%) were adults (median age 53.7 years [IQR 34.0-65.7]) and 53 (73%) were children (median age 1.9 years [IQR 0.2-4.0]). The proportion of adults increased from 12% in 2014 to 48% in 2018 (p = 0.01). All adults had an underlying comorbidity factor, including chronic lung disease in 12 (60%), diabetes mellitus in six (30%), and chronic heart disease in five (25%). Clade D1 infected a higher proportion of adults than clades B3 and B2 (p = 0.001). Clade D1 was more divergent than clade B3: 5 of 19 amino acid changes in the capsid proteins were located in putative antigenic sites. Adult patients with underlying conditions are more likely to present with severe complications associated with EV-D68, notably the emergent clade D1.
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Affiliation(s)
- Maxime Duval
- Université Clermont Auvergne, LMGE CNRS 6023, UFR de Médecine et des Professions Paramédicales, 63001 Clermont-Ferrand, France; (M.D.); (A.M.); (G.J.); (M.B.); (C.A.); (C.H.)
| | - Audrey Mirand
- Université Clermont Auvergne, LMGE CNRS 6023, UFR de Médecine et des Professions Paramédicales, 63001 Clermont-Ferrand, France; (M.D.); (A.M.); (G.J.); (M.B.); (C.A.); (C.H.)
- CHU Clermont-Ferrand, Centre National de Référence Des Entérovirus et Parechovirus, Laboratoire de Virologie, 63003 Clermont-Ferrand, France
| | - Olivier Lesens
- CHU Clermont-Ferrand, Service Des Maladies Infectieuses et Tropicales, 63003 Clermont-Ferrand, France;
| | - Jacques-Olivier Bay
- CHU Clermont-Ferrand, Service de Thérapie Cellulaire et Hématologie Clinique, 63003 Clermont-Ferrand, France;
| | - Denis Caillaud
- CHU Clermont-Ferrand, Service de Pneumologie, 63003 Clermont-Ferrand, France;
| | - Denis Gallot
- CHU Clermont-Ferrand, Service de Gynécologie-Obstétrique, 63003 Clermont-Ferrand, France;
| | | | - Sylvie Montcouquiol
- CHU Clermont-Ferrand, Centre de Référence et de Compétence Mucoviscidose, 63003 Clermont-Ferrand, France;
| | - Jeannot Schmidt
- CHU Clermont-Ferrand, Service Des Urgences, 63003 Clermont-Ferrand, France;
| | - Carole Egron
- CHU Clermont-Ferrand, Service de Pédiatrie Générale, 63003 Clermont-Ferrand, France;
| | - Gwendoline Jugie
- Université Clermont Auvergne, LMGE CNRS 6023, UFR de Médecine et des Professions Paramédicales, 63001 Clermont-Ferrand, France; (M.D.); (A.M.); (G.J.); (M.B.); (C.A.); (C.H.)
| | - Maxime Bisseux
- Université Clermont Auvergne, LMGE CNRS 6023, UFR de Médecine et des Professions Paramédicales, 63001 Clermont-Ferrand, France; (M.D.); (A.M.); (G.J.); (M.B.); (C.A.); (C.H.)
- CHU Clermont-Ferrand, Centre National de Référence Des Entérovirus et Parechovirus, Laboratoire de Virologie, 63003 Clermont-Ferrand, France
| | - Christine Archimbaud
- Université Clermont Auvergne, LMGE CNRS 6023, UFR de Médecine et des Professions Paramédicales, 63001 Clermont-Ferrand, France; (M.D.); (A.M.); (G.J.); (M.B.); (C.A.); (C.H.)
- CHU Clermont-Ferrand, Centre National de Référence Des Entérovirus et Parechovirus, Laboratoire de Virologie, 63003 Clermont-Ferrand, France
| | - Céline Lambert
- CHU Clermont-Ferrand, Service Biométrie et Médico-Economie—Direction de la Recherche Clinique et Innovation, 63003 Clermont-Ferrand, France;
| | - Cécile Henquell
- Université Clermont Auvergne, LMGE CNRS 6023, UFR de Médecine et des Professions Paramédicales, 63001 Clermont-Ferrand, France; (M.D.); (A.M.); (G.J.); (M.B.); (C.A.); (C.H.)
- CHU Clermont-Ferrand, Centre National de Référence Des Entérovirus et Parechovirus, Laboratoire de Virologie, 63003 Clermont-Ferrand, France
| | - Jean-Luc Bailly
- Université Clermont Auvergne, LMGE CNRS 6023, UFR de Médecine et des Professions Paramédicales, 63001 Clermont-Ferrand, France; (M.D.); (A.M.); (G.J.); (M.B.); (C.A.); (C.H.)
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12
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Sanjay RE, Sabeena S, Robin S, Shaji JT, Jayakrishnan MP, Suresh EKK, Michael CJ, Aswathyraj S, Josmi J, Shahin S, Anup J, Arunkumar G. Genetic analysis of Enterovirus D68 associated with pneumonia in children from South India. J Med Microbiol 2021; 70. [PMID: 33999799 DOI: 10.1099/jmm.0.001356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
EV-D68 is an emerging enterovirus infection associated with severe acute respiratory illness (SARI), acute flaccid myelitis (AFM) and acute flaccid paralysis (AFP). While EV-D68 outbreaks and sporadic cases are reported globally, a single case has been reported from India. The present study aims to investigate the molecular epidemiology and clinical characteristics of EV-D68-associated SARI cases from South India. We screened influenza-negative archived throat swab specimens from Influenza-Like Illness (ILI) and SARI cases (n=959; 2016 to 2018 period) for enteroviruses by pan-enterovirus real-time RT-PCR. Thirteen samples positive for enteroviruses were typed by PCR and sequencing based on VPI, VP2 and/or 5'NCR regions. One EV-D68 RNA sample was subjected to next-generation sequencing for whole genome characterisation. Among 13 enterovirus cases, four were ECHO-11, three EV-D68, two CV-A16 and one each EV-71, CV-B1, CV-B2 and CV-A9. All three cases of EV-D68 infection were reported in children below 2 years of age from Kerala state of South India during June and July 2017. The patients developed pneumonia without any neurological complications. Sequencing based on VPI and 5'NCR regions showed that EV-D68 strains belong to the novel subclade B3. The EV-D68 complete genome identified with two unique amino acid substitutions in VP1 (T-246-I) and 3D (K-344-R) regions. This study reiterates the EV-D68 novel subclade B3 circulation in India and indicates the urgent need for structured EV-D68 surveillance in the country to describe the epidemiology.
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Affiliation(s)
- Ramachandran Erathodi Sanjay
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Sasidharanpillai Sabeena
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Sudandiradas Robin
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - John T Shaji
- Department of Paediatrics & Neonatology, Baby Memorial Hospital, Kozhikode, Kerala, India
| | - M P Jayakrishnan
- Department of Paediatrics, Government Medical College, Kozhikode, Kerala, India
| | - E K Kumar Suresh
- Department of Paediatrics, Aster MIMS Hospital, Kozhikode, Kerala, India
| | - C J Michael
- Department of ENT, Government General Hospital, Kozhikode, Kerala, India
| | - S Aswathyraj
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Joseph Josmi
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Sheik Shahin
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Jayaram Anup
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Govindakarnavar Arunkumar
- Present address: Consultant at World Health Organisation- country office for Nepal, Nepal, India.,Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
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13
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Elrick MJ, Pekosz A, Duggal P. Enterovirus D68 molecular and cellular biology and pathogenesis. J Biol Chem 2021; 296:100317. [PMID: 33484714 PMCID: PMC7949111 DOI: 10.1016/j.jbc.2021.100317] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
In recent years, enterovirus D68 (EV-D68) has advanced from a rarely detected respiratory virus to a widespread pathogen responsible for increasing rates of severe respiratory illness and acute flaccid myelitis (AFM) in children worldwide. In this review, we discuss the accumulating data on the molecular features of EV-D68 and place these into the context of enterovirus biology in general. We highlight similarities and differences with other enteroviruses and genetic divergence from own historical prototype strains of EV-D68. These include changes in capsid antigens, host cell receptor usage, and viral RNA metabolism collectively leading to increased virulence. Furthermore, we discuss the impact of EV-D68 infection on the biology of its host cells, and how these changes are hypothesized to contribute to motor neuron toxicity in AFM. We highlight areas in need of further research, including the identification of its primary receptor and an understanding of the pathogenic cascade leading to motor neuron injury in AFM. Finally, we discuss the epidemiology of the EV-D68 and potential therapeutic approaches.
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Affiliation(s)
- Matthew J Elrick
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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14
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Brown DM, Zhang Y, Scheuermann RH. Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses. Microorganisms 2020; 8:microorganisms8121856. [PMID: 33255654 PMCID: PMC7759938 DOI: 10.3390/microorganisms8121856] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses (EVs) are positive-sense RNA viruses, with over 50,000 nucleotide sequences publicly available. While most human infections are typically associated with mild respiratory symptoms, several different EV types have also been associated with severe human disease, especially acute flaccid paralysis (AFP), particularly with endemic members of the EV-B species and two pandemic types—EV-A71 and EV-D68—that appear to be responsible for recent widespread outbreaks. Here we review the recent literature on the prevalence, characteristics, and circulation dynamics of different enterovirus types and combine this with an analysis of the sequence coverage of different EV types in public databases (e.g., the Virus Pathogen Resource). This evaluation reveals temporal and geographic differences in EV circulation and sequence distribution, highlighting recent EV outbreaks and revealing gaps in sequence coverage. Phylogenetic analysis of the EV genus shows the relatedness of different EV types. Recombination analysis of the EV-A species provides evidence for recombination as a mechanism of genomic diversification. The absence of broadly protective vaccines and effective antivirals makes human enteroviruses important pathogens of public health concern.
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Affiliation(s)
- David M Brown
- Department of Synthetic Biology, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- La Jolla Institute for Immunology, La Jolla, CA 92065, USA
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15
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Han Z, Song Y, Xiao J, Jiang L, Huang W, Wei H, Li J, Zeng H, Yu Q, Li J, Yu D, Zhang Y, Li C, Zhan Z, Shi Y, Xiong Y, Wang X, Ji T, Yang Q, Zhu S, Yan D, Xu W, Zhang Y. Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000-18. Virus Evol 2020; 6:veaa084. [PMID: 33343924 PMCID: PMC7733612 DOI: 10.1093/ve/veaa084] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hand, foot, and mouth disease (HFMD), which is a frequently reported and concerning disease worldwide, is a severe burden on societies globally, especially in the countries of East and Southeast Asia. Coxsackievirus A16 (CV-A16) is one of the most important causes of HFMD and a severe threat to human health, especially in children under 5 years of age. To investigate the epidemiological characteristics, spread dynamics, recombinant forms (RFs), and other features of CV-A16, we leveraged the continuous surveillance data of CV-A16-related HFMD cases collected over an 18-year period. With the advent of the EV-A71 vaccine since 2016, which targeted the EV-A71-related HFMD cases, EV-A71-related HFMD cases decreased dramatically, whereas the CV-A16-related HFMD cases showed an upward trend from 2017 to October 2019. The CV-A16 strains observed in this study were genetically related and widely distributed in the mainland of China. Our results show that three clusters (B1a-B1c) existed in the mainland of China and that the cluster of B1b dominates the diffusion of CV-A16 in China. We found that eastern China played a decisive role in seeding the diffusion of CV-A16 in China, with a more complex and variant transmission trend. Although EV-A71 vaccine was launched in China in 2016, it did not affect the genetic diversity of CV-A16, and its genetic diversity did not decline, which confirmed the epidemiological surveillance trend of CV-A16. Two discontinuous clusters (2000-13 and 2014-18) were observed in the full-length genome and arranged along the time gradient, which revealed the reason why the relative genetic diversity of CV-A16 increased and experienced more complex fluctuation model after 2014. In addition, the switch from RFs B (RF-B) and RF-C co-circulation to RF-D contributes to the prevalence of B1b cluster in China after 2008. The correlation between genotype and RFs partially explained the current prevalence of B1b. This study provides unprecedented full-length genomic sequences of CV-A16 in China, with a wider geographic distribution and a long-term time scale. The study presents valuable information about CV-A16, aimed at developing effective control strategies, as well as a call for a more robust surveillance system, especially in the Asia-Pacific region.
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Affiliation(s)
- Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Lili Jiang
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Wei Huang
- Chongqing Center for Disease Control and Prevention, Chongqing City, People's Republic of China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, People's Republic of China
| | - Jie Li
- Beijing Center for Disease Control and Prevention, Beijing City, People's Republic of China
| | - Hanri Zeng
- Guangdong Center for Disease Control and Prevention, Guangzhou, Guangdong Province, People's Republic of China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, People's Republic of China
| | - Jiameng Li
- Tianjin Center for Disease Control and Prevention, Tianjin City, People's Republic of China
| | - Deshan Yu
- Gansu Center for Disease Control and Prevention, Lanzhou, Gansu Province, People's Republic of China
| | - Yanjun Zhang
- Zhejiang Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, People's Republic of China
| | - Chonghai Li
- Qinghai Center for Disease Control and Prevention, Xining, Qinghai Province, People's Republic of China
| | - Zhifei Zhan
- Hunan Center for Disease Control and Prevention, Changsha, Hunan Province, People's Republic of China
| | - Yonglin Shi
- Anhui Center for Disease Control and Prevention, Hefei, Anhui Province, People's Republic of China
| | - Ying Xiong
- Jiangxi Center for Disease Control and Prevention, Nanchang, Jiangxi Province, People's Republic of China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, People's Republic of China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, People's Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, People's Republic of China
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16
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Kempf BJ, Watkins CL, Peersen OB, Barton DJ. An Extended Primer Grip of Picornavirus Polymerase Facilitates Sexual RNA Replication Mechanisms. J Virol 2020; 94:e00835-20. [PMID: 32522851 PMCID: PMC7394906 DOI: 10.1128/jvi.00835-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/02/2020] [Indexed: 11/20/2022] Open
Abstract
Picornaviruses have both asexual and sexual RNA replication mechanisms. Asexual RNA replication mechanisms involve one parental template, whereas sexual RNA replication mechanisms involve two or more parental templates. Because sexual RNA replication mechanisms counteract ribavirin-induced error catastrophe, we selected for ribavirin-resistant poliovirus to identify polymerase residues that facilitate sexual RNA replication mechanisms. We used serial passage in ribavirin, beginning with a variety of ribavirin-sensitive and ribavirin-resistant parental viruses. Ribavirin-sensitive virus contained an L420A polymerase mutation, while ribavirin-resistant virus contained a G64S polymerase mutation. A G64 codon mutation (G64Fix) was used to inhibit emergence of G64S-mediated ribavirin resistance. Revertants (L420) or pseudorevertants (L420V and L420I) were selected from all independent lineages of L420A, G64Fix L420A, and G64S L420A parental viruses. Ribavirin resistance G64S mutations were selected in two independent lineages, and novel ribavirin resistance mutations were selected in the polymerase in other lineages (M299I, M323I, M392V, and T353I). The structural orientation of M392, immediately adjacent to L420 and the polymerase primer grip region, led us to engineer additional polymerase mutations into poliovirus (M392A, M392L, M392V, K375R, and R376K). L420A revertants and pseudorevertants (L420V and L420I) restored efficient viral RNA recombination, confirming that ribavirin-induced error catastrophe coincides with defects in sexual RNA replication mechanisms. Viruses containing M392 mutations (M392A, M392L, and M392V) and primer grip mutations (K375R and R376K) exhibited divergent RNA recombination, ribavirin sensitivity, and biochemical phenotypes, consistent with changes in the fidelity of RNA synthesis. We conclude that an extended primer grip of the polymerase, including L420, M392, K375, and R376, contributes to the fidelity of RNA synthesis and to efficient sexual RNA replication mechanisms.IMPORTANCE Picornaviruses have both asexual and sexual RNA replication mechanisms. Sexual RNA replication shapes picornavirus species groups, contributes to the emergence of vaccine-derived polioviruses, and counteracts error catastrophe. Can viruses distinguish between homologous and nonhomologous partners during sexual RNA replication? We implicate an extended primer grip of the viral polymerase in sexual RNA replication mechanisms. By sensing RNA sequence complementarity near the active site, the extended primer grip of the polymerase has the potential to distinguish between homologous and nonhomologous RNA templates during sexual RNA replication.
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Affiliation(s)
- Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Colorado, USA
| | - Colleen L Watkins
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Colorado, USA
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17
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Bal A, Sabatier M, Wirth T, Coste-Burel M, Lazrek M, Stefic K, Brengel-Pesce K, Morfin F, Lina B, Schuffenecker I, Josset L. Emergence of enterovirus D68 clade D1, France, August to November 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 30670143 PMCID: PMC6344839 DOI: 10.2807/1560-7917.es.2019.24.3.1800699] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report a seasonal increase of enterovirus D68 (EV-D68) cases in France, with 54 cases detected between 19 August and 14 November 2018. Molecular typing revealed that 20 of 32 of the isolates belonged to clade D1, only sporadically detected before in France. Median age of D1-cases was 42 years, 10 developed severe respiratory signs and one had neurological complications. The 2018-D1 viruses showed a genetic divergence of 3.34 % with D1 viruses identified previously.
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Affiliation(s)
- Antonin Bal
- Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France.,Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Marina Sabatier
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Thierry Wirth
- Institut Systématique, Evolution, Biodiversité (ISYEB), EPHE, MNHN, CNRS, Sorbonne Université, Paris, France.,Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, EPHE, PSL Université, Paris, France
| | - Marianne Coste-Burel
- Laboratoire de Virologie, UIC9 CIC infectieux, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Mouna Lazrek
- Laboratoire de Virologie, EA3610, Centre Hospitalier Universitaire de Lille, Université de Lille, Lille, France
| | - Karl Stefic
- Laboratoire de Virologie and CNR VIH-Laboratoire Associé, Centre Hospitalier Régional Universitaire de Tours, Tours, France.,INSERM U1259, Université de Tours, Tours, France
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Florence Morfin
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Bruno Lina
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Isabelle Schuffenecker
- Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
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18
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Vogt MR, Fu J, Kose N, Williamson LE, Bombardi R, Setliff I, Georgiev IS, Klose T, Rossmann MG, Bochkov YA, Gern JE, Kuhn RJ, Crowe JE. Human antibodies neutralize enterovirus D68 and protect against infection and paralytic disease. Sci Immunol 2020; 5:5/49/eaba4902. [PMID: 32620559 DOI: 10.1126/sciimmunol.aba4902] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 06/12/2020] [Indexed: 12/17/2022]
Abstract
Enterovirus D68 (EV-D68) causes outbreaks of respiratory illness, and there is increasing evidence that it causes outbreaks of acute flaccid myelitis (AFM). There are no licensed therapies to prevent or treat EV-D68 infection or AFM disease. We isolated a panel of EV-D68-reactive human monoclonal antibodies that recognize diverse antigenic variants from participants with prior infection. One potently neutralizing cross-reactive antibody, EV68-228, protected mice from respiratory and neurologic disease when given either before or after infection. Cryo-electron microscopy studies revealed that EV68-228 and another potently neutralizing antibody (EV68-159) bound around the fivefold or threefold axes of symmetry on virion particles, respectively. The structures suggest diverse mechanisms of action by these antibodies. The high potency and effectiveness observed in vivo suggest that antibodies are a mechanistic correlate of protection against AFM disease and are candidates for clinical use in humans with EV-D68 infection.
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Affiliation(s)
- Matthew R Vogt
- Department of Pediatrics (Infectious Diseases), Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jianing Fu
- Department of Biological Sciences and Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren E Williamson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin Bombardi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ian Setliff
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas Klose
- Department of Biological Sciences and Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Michael G Rossmann
- Department of Biological Sciences and Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Richard J Kuhn
- Department of Biological Sciences and Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - James E Crowe
- Department of Pediatrics (Infectious Diseases), Vanderbilt University Medical Center, Nashville, TN, USA. .,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA
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19
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Meyers L, Dien Bard J, Galvin B, Nawrocki J, Niesters HGM, Stellrecht KA, St George K, Daly JA, Blaschke AJ, Robinson C, Wang H, Cook CV, Hassan F, Dominguez SR, Pretty K, Naccache S, Olin KE, Althouse BM, Jones JD, Ginocchio CC, Poritz MA, Leber A, Selvarangan R. Enterovirus D68 outbreak detection through a syndromic disease epidemiology network. J Clin Virol 2020; 124:104262. [PMID: 32007841 DOI: 10.1016/j.jcv.2020.104262] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND In 2014, enterovirus D68 (EV-D68) was responsible for an outbreak of severe respiratory illness in children, with 1,153 EV-D68 cases reported across 49 states. Despite this, there is no commercial assay for its detection in routine clinical care. BioFire® Syndromic Trends (Trend) is an epidemiological network that collects, in near real-time, deidentified. BioFire test results worldwide, including data from the BioFire® Respiratory Panel (RP). OBJECTIVES Using the RP version 1.7 (which was not explicitly designed to differentiate EV-D68 from other picornaviruses), we formulate a model, Pathogen Extended Resolution (PER), to distinguish EV-D68 from other human rhinoviruses/enteroviruses (RV/EV) tested for in the panel. Using PER in conjunction with Trend, we survey for historical evidence of EVD68 positivity and demonstrate a method for prospective real-time outbreak monitoring within the network. STUDY DESIGN PER incorporates real-time polymerase chain reaction metrics from the RPRV/EV assays. Six institutions in the United States and Europe contributed to the model creation, providing data from 1,619 samples spanning two years, confirmed by EV-D68 gold-standard molecular methods. We estimate outbreak periods by applying PER to over 600,000 historical Trend RP tests since 2014. Additionally, we used PER as a prospective monitoring tool during the 2018 outbreak. RESULTS The final PER algorithm demonstrated an overall sensitivity and specificity of 87.1% and 86.1%, respectively, among the gold-standard dataset. During the 2018 outbreak monitoring period, PER alerted the research network of EV-D68 emergence in July. One of the first sites to experience a significant increase, Nationwide Children's Hospital, confirmed the outbreak and implemented EV-D68 testing at the institution in response. Applying PER to the historical Trend dataset to determine rates among RP tests, we find three potential outbreaks with predicted regional EV-D68 rates as high as 37% in 2014, 16% in 2016, and 29% in 2018. CONCLUSIONS Using PER within the Trend network was shown to both accurately predict outbreaks of EV-D68 and to provide timely notifications of its circulation to participating clinical laboratories.
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Affiliation(s)
- Lindsay Meyers
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA 90039, United States.
| | - Ben Galvin
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jeff Nawrocki
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Hubert G M Niesters
- The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands.
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY 12208, United States.
| | - Kirsten St George
- New York State Department of Health, Albany, NY, 12202, United States.
| | - Judy A Daly
- Department of Pathology, University of Utah, Salt Lake City, UT 84132, United States; Division of Inpatient Medicine, Primary Children's Hospital, Salt Lake City, UT 84132, United States.
| | - Anne J Blaschke
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, United States.
| | - Christine Robinson
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Huanyu Wang
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Camille V Cook
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Ferdaus Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
| | - Sam R Dominguez
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Kristin Pretty
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Samia Naccache
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States.
| | | | - Benjamin M Althouse
- Information School, University of Washington, Seattle, WA, 98105, United States; Department of Biology, New Mexico State University, Las Cruces, NM, 88003, United States.
| | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States; Global Medical Affairs, bioMérieux, Durham, NC 27712, United States; Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, United States.
| | - Mark A Poritz
- BioFire Defense, Salt Lake City, UT 84107, United States.
| | - Amy Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
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20
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Nearly Complete Genome Sequences of 17 Enterovirus D68 Strains from Kansas City, Missouri, 2018. Microbiol Resour Announc 2019; 8:8/45/e00388-19. [PMID: 31699753 PMCID: PMC6838611 DOI: 10.1128/mra.00388-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report 17 nearly complete genome sequences of enterovirus D68 (EV-D68) isolated from Kansas City, MO, in 2018. Phylogenetic analysis suggests that these strains belong to subclade B3, similar to the ones that caused the 2016 epidemics in the United States but different from the 2014 outbreak B1 strains.
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21
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Neurotropism of Enterovirus D68 Isolates Is Independent of Sialic Acid and Is Not a Recently Acquired Phenotype. mBio 2019; 10:mBio.02370-19. [PMID: 31641090 PMCID: PMC6805996 DOI: 10.1128/mbio.02370-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Since 2014, numerous outbreaks of childhood infections with enterovirus D68 (EV-D68) have occurred worldwide. Most infections are associated with flu-like symptoms, but paralysis may develop in young children. It has been suggested that infection only with recent viral isolates can cause paralysis. To address the hypothesis that EV-D68 has recently acquired neurotropism, murine organotypic brain slice cultures, induced human motor neurons and astrocytes, and mice lacking the alpha/beta interferon receptor were infected with multiple virus isolates. All EV-D68 isolates, from 1962 to the present, can infect neural cells, astrocytes, and neurons. Furthermore, our results show that sialic acid binding does not play a role in EV-D68 neuropathogenesis. The study of EV-D68 infection in organotypic brain slice cultures, induced motor neurons, and astrocytes will allow for the elucidation of the mechanism by which the virus infection causes disease. Acute flaccid myelitis (AFM) is a rare but serious illness of the nervous system, specifically affecting the gray matter of the spinal cord, motor-controlling regions of the brain, and cranial nerves. Most cases of AFM are pathogen associated, typically with poliovirus and enterovirus infections, and occur in children under the age of 6 years. Enterovirus D68 (EV-D68) was first isolated from children with pneumonia in 1962, but an association with AFM was not observed until the 2014 outbreak. Organotypic mouse brain slice cultures generated from postnatal day 1 to 10 mice and adult ifnar knockout mice were used to determine if neurotropism of EV-D68 is shared among virus isolates. All isolates replicated in organotypic mouse brain slice cultures, and three isolates replicated in primary murine astrocyte cultures. All four EV-D68 isolates examined caused paralysis and death in adult ifnar knockout mice. In contrast, no viral disease was observed after intracranial inoculation of wild-type mice. Six of the seven EV-D68 isolates, including two from 1962 and four from the 2014 outbreak, replicated in induced human neurons, and all of the isolates replicated in induced human astrocytes. Furthermore, a putative viral receptor, sialic acid, is not required for neurotropism of EV-D68, as viruses replicated within neurons and astrocytes independent of binding to sialic acid. These observations demonstrate that EV-D68 is neurotropic independent of its genetic lineage and can infect both neurons and astrocytes and that neurotropism is not a recently acquired characteristic as has been suggested. Furthermore, the results show that in mice the innate immune response is critical for restricting EV-D68 disease.
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22
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Gonzalez G, Carr MJ, Kobayashi M, Hanaoka N, Fujimoto T. Enterovirus-Associated Hand-Foot and Mouth Disease and Neurological Complications in Japan and the Rest of the World. Int J Mol Sci 2019; 20:ijms20205201. [PMID: 31635198 PMCID: PMC6834195 DOI: 10.3390/ijms20205201] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
Enteroviruses (EVs) are responsible for extremely large-scale, periodic epidemics in pediatric cohorts, particularly in East and Southeast Asia. Clinical presentation includes a diverse disease spectrum, including hand-foot and mouth disease (HFMD), aseptic meningitis, encephalitis, acute flaccid paralysis, and acute flaccid myelitis. HFMD is predominantly attributable to EV-A types, including the major pathogen EV-A71, and coxsackieviruses, particularly CV-A6, CV-A16, and CV-A10. There have been multiple EV-A71 outbreaks associated with a profound burden of neurological disease and fatal outcomes in Asia since the early 1980s. Efficacious vaccines against EV-A71 have been developed in China but widespread pediatric vaccination programs have not been introduced in other countries. Encephalitis, as a consequence of complications arising from HFMD infection, leads to damage to the thalamus and medulla oblongata. Studies in Vietnam suggest that myoclonus is a significant indicator of central nervous system (CNS) complications in EV-A71-associated HFMD cases. Rapid response in HFMD cases in children is imperative to prevent the progression to a CNS infection; however, prophylactic and therapeutic agents have not been well established internationally, therefore surveillance and functional studies including development of antivirals and multivalent vaccines is critically important to reduce disease burden in pediatric populations.
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Affiliation(s)
- Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan.
- National Advanced Computing Collaboratory, National Center for High Technology, San Jose 1174-1200, Costa Rica.
| | - Michael J Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland.
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0020, Japan.
| | | | - Nozomu Hanaoka
- Division 4, Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Tsuguto Fujimoto
- Division 4, Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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23
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Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses 2019; 11:E859. [PMID: 31540135 PMCID: PMC6784155 DOI: 10.3390/v11090859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/15/2023] Open
Abstract
RNA recombination is a major driving force in the evolution and genetic architecture shaping of enteroviruses. In particular, intertypic recombination is implicated in the emergence of most pathogenic circulating vaccine-derived polioviruses, which have caused numerous outbreaks of paralytic poliomyelitis worldwide. Recent experimental studies that relied on recombination cellular systems mimicking natural genetic exchanges between enteroviruses provided new insights into the molecular mechanisms of enterovirus recombination and enabled to define a new model of genetic plasticity for enteroviruses. Homologous intertypic recombinant enteroviruses that were observed in nature would be the final products of a multi-step process, during which precursor nonhomologous recombinant genomes are generated through an initial inter-genomic RNA recombination event and can then evolve into a diversity of fitter homologous recombinant genomes over subsequent intra-genomic rearrangements. Moreover, these experimental studies demonstrated that the enterovirus genome could be defined as a combination of genomic modules that can be preferentially exchanged through recombination, and enabled defining the boundaries of these recombination modules. These results provided the first experimental evidence supporting the theoretical model of enterovirus modular evolution previously elaborated from phylogenetic studies of circulating enterovirus strains. This review summarizes our current knowledge regarding the mechanisms of recombination in enteroviruses and presents a new evolutionary process that may apply to other RNA viruses.
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Affiliation(s)
- Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito EC170125, Pichincha, Ecuador.
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Bruno Blondel
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
| | - Francis Delpeyroux
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
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24
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Hixon AM, Frost J, Rudy MJ, Messacar K, Clarke P, Tyler KL. Understanding Enterovirus D68-Induced Neurologic Disease: A Basic Science Review. Viruses 2019; 11:E821. [PMID: 31487952 PMCID: PMC6783995 DOI: 10.3390/v11090821] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 12/28/2022] Open
Abstract
In 2014, the United States (US) experienced an unprecedented epidemic of enterovirus D68 (EV-D68)-induced respiratory disease that was temporally associated with the emergence of acute flaccid myelitis (AFM), a paralytic disease occurring predominantly in children, that has a striking resemblance to poliomyelitis. Although a definitive causal link between EV-D68 infection and AFM has not been unequivocally established, rapidly accumulating clinical, immunological, and epidemiological evidence points to EV-D68 as the major causative agent of recent seasonal childhood AFM outbreaks in the US. This review summarizes evidence, gained from in vivo and in vitro models of EV-D68-induced disease, which demonstrates that contemporary EV-D68 strains isolated during and since the 2014 outbreak differ from historical EV-D68 in several factors influencing neurovirulence, including their genomic sequence, their receptor utilization, their ability to infect neurons, and their neuropathogenicity in mice. These findings provide biological plausibility that EV-D68 is a causal agent of AFM and provide important experimental models for studies of pathogenesis and treatment that are likely to be difficult or impossible in humans.
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Affiliation(s)
- Alison M Hixon
- Medical Scientist Training Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Joshua Frost
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michael J Rudy
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kevin Messacar
- Hospital Medicine and Pediatric Infectious Disease Sections, Department of Pediatrics, University of Colorado, Aurora, CO 80045, USA.
- Children's Hospital Colorado, Aurora, CO 80045, USA.
| | - Penny Clarke
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Kenneth L Tyler
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Division of Infectious Disease, Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Neurology Service, Rocky Mountain VA Medical Center, Aurora, CO 80045, USA
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25
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Detection of Enteroviruses in Children with Acute Diarrhea. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.83916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Funakoshi Y, Ito K, Morino S, Kinoshita K, Morikawa Y, Kono T, Doan YH, Shimizu H, Hanaoka N, Konagaya M, Fujimoto T, Suzuki A, Chiba T, Akiba T, Tomaru Y, Watanabe K, Shimizu N, Horikoshi Y. Enterovirus D68 respiratory infection in a children's hospital in Japan in 2015. Pediatr Int 2019; 61:768-776. [PMID: 31136073 PMCID: PMC7167638 DOI: 10.1111/ped.13903] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 02/22/2019] [Accepted: 04/04/2019] [Indexed: 01/18/2023]
Abstract
BACKGROUND Outbreaks of enterovirus D68 (EV-D68) respiratory infections in children were reported globally in 2014. In Japan, there was an EV-D68 outbreak in the autumn of 2015 (September-October). The aim of this study was to compare EV-D68-specific polymerase chain reaction (PCR)-positive and EV-D68-specific PCR-negative patients. METHODS Pediatric patients admitted for any respiratory symptoms between September and October 2015 were enrolled. Nasopharyngeal swabs were tested for multiplex respiratory virus PCR and EV-D68-specific reverse transcription-PCR. EV-D68-specific PCR-positive and -negative patients were compared regarding demographic data and clinical information. RESULTS A nasopharyngeal swab was obtained from 76 of 165 patients admitted with respiratory symptoms during the study period. EV-D68 was detected in 40 samples (52.6%). Median age in the EV-D68-specific PCR-positive and -negative groups was 3.0 years (IQR, 5.5 years) and 3.0 years (IQR, 4.0 years), respectively. The rates of coinfection in the two groups were 32.5% and 47.2%, respectively. There was no significant difference in the history of asthma or recurrent wheezing, length of hospitalization, or pediatric intensive care unit admission rate between the groups. The median days between symptom onset and admission was significantly lower for the EV-D68-positive group (3.0 days vs 5.0 days, P = 0.001). EV-D68 was identified as clade B on phylogenetic analysis. No cases of acute flaccid myelitis were encountered. CONCLUSIONS More than half of the samples from the children admitted with respiratory symptoms were positive for EV-D68-specific PCR during the outbreak. Asthma history was not associated with the risk of developing severe respiratory infection.
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Affiliation(s)
- Yu Funakoshi
- Department of General Pediatrics, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Kenta Ito
- Division of Infectious Diseases, Department of Pediatrics, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Saeko Morino
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Kazue Kinoshita
- Division of Infectious Diseases, Department of Pediatrics, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Yoshihiko Morikawa
- Clinical Research Support Center, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Tatsuo Kono
- Department of Radiology, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Nozomu Hanaoka
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Masami Konagaya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Tsuguto Fujimoto
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Ai Suzuki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku, Tokyo, Japan
| | - Takashi Chiba
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku, Tokyo, Japan
| | - Tetsuya Akiba
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku, Tokyo, Japan
| | - Yasuhiro Tomaru
- Division of Medical Science, Department of Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Ken Watanabe
- Division of Medical Science, Department of Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Norio Shimizu
- Division of Medical Science, Department of Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Yuho Horikoshi
- Division of Infectious Diseases, Department of Pediatrics, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
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27
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Klaiber N, McVoy MA, Zhao W. Susceptibility of Enterovirus-D68 to RNAi-mediated antiviral knockdown. Antiviral Res 2019; 170:104565. [PMID: 31336148 DOI: 10.1016/j.antiviral.2019.104565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/17/2019] [Accepted: 07/20/2019] [Indexed: 01/22/2023]
Abstract
Enterovirus D68 (EV-D68) represents an emerging pathogen which has demonstrated a capacity for causing epidemic illness in pediatric and immunocompromised patients. With no effective antiviral treatment available, therapeutic interventions are currently limited to supportive care. Utilizing available genomic sequences from the 2014 B3 Epidemic EV-D68 clade and the 1962 Fermon EV-D68 strains, we performed in silico comparative genomic analysis, identifying several islands of phylogenetic conservation within the viral RNA-dependent RNA polymerase gene. The effects of transfecting short-interfering double-stranded RNA (siRNA) molecules targeting these conserved sequences were tested in vitro using a human rhabdomyosarcoma cell-based model of EV-D68 infection. Two siRNA sequences demonstrated reproducible ability to abrogate EV-D68-mediated cytopathic effect in vitro. These siRNA sequences were also able to decrease EV-D68 genome replication, VP-2 capsid protein expression, and infectious particle production in vitro. EV-D68 knockdown was sequence-specific and not observed in cells treated with a negative control siRNA lacking sequence homology to the viral genome. The regions targeted by these siRNA's are located in highly conserved regions of the RNA-dependent RNA polymerase gene. The most potent siRNA targeted a sequence found in subsequent enzyme crystallographic studies to enhance the enzyme's thermostability (Wang et al., 2017). Topical nebulized siRNAs have recently been utilized as antivirals in human studies, with no adverse effects or toxicities noted (Gottlieb et al., 2016). Sequence selection is likely one primary factor determining the potential efficacy of such therapeutics. These results demonstrate that the identified siRNA sequences are able to suppress EV-D68 replication and cytopathic effect in vitro.
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Affiliation(s)
- Nicholas Klaiber
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael A McVoy
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, USA
| | - Wei Zhao
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, USA.
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28
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Furuse Y, Chaimongkol N, Okamoto M, Oshitani H. Evolutionary and Functional Diversity of the 5' Untranslated Region of Enterovirus D68: Increased Activity of the Internal Ribosome Entry Site of Viral Strains during the 2010s. Viruses 2019; 11:v11070626. [PMID: 31288421 PMCID: PMC6669567 DOI: 10.3390/v11070626] [Citation(s) in RCA: 9] [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: 06/24/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 12/14/2022] Open
Abstract
The 5′ untranslated region (UTR) of the RNA genomes of enteroviruses possesses an internal ribosome entry site (IRES) that directs translation of the mRNA by binding to ribosomes. Infection with enterovirus D68 causes respiratory symptoms and is sometimes associated with neurological disorders. The number of reports of the viral infection and neurological disorders has increased in 2010s, although the reason behind this phenomenon remains unelucidated. In this study, we investigated the evolutionary and functional diversity of the 5′ UTR of recently circulating strains of the virus. Genomic sequences of 374 viral strains were acquired and subjected to phylogenetic analysis. The IRES activity of the viruses was measured using a luciferase reporter assay. We found a highly conserved sequence in the 5′ UTR and also identified the location of variable sites in the predicted RNA secondary structure. IRES activities differed among the strains in some cell lines, including neuronal and respiratory cells, and were especially high in strains of a major lineage from the recent surge. The effect of mutations in the 5′ UTR should be studied further in the future for better understanding of viral pathogenesis.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawaracho, Sakyo-ku, Kyoto 606-8507, Japan.
- Hakubi Center for Advanced Research, Kyoto University, Yoshidahonmachi, Sakyo-ku, Kyoto 606-8501, Japan.
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan.
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan.
| | - Natthawan Chaimongkol
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
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29
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Chien YS, Luo ST, Tsao KC, Huang YC, Chung WY, Liao YC, Tan Y, Das SR, Lee MS. Genomic analysis of serologically untypable human enteroviruses in Taiwan. J Biomed Sci 2019; 26:49. [PMID: 31266491 PMCID: PMC6607526 DOI: 10.1186/s12929-019-0541-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/11/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Human enteroviruses contain over 100 serotypes. We have routinely conducted enterovirus surveillance in northern Taiwan; but about 10% of isolates could not be serotyped using traditional assays. Next-generation sequencing (NGS) is a powerful tool for genome sequencing. METHODS In this study, we established an NGS platform to conduct genome sequencing for the serologically untypable enterovirus isolates. RESULTS Among 130 serologically untypable isolates, 121 (93%) of them were classified into 29 serotypes using CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer)-based RT-PCR to amplify VP1 genes (VP1-CODEHOP). We further selected 52 samples for NGS and identified 59 genome sequences from 51 samples, including 8 samples containing two virus genomes. We also detected 23 genome variants (nucleotide identity < 90% compared with genome sequences in the public domain) which were potential genetic recombination, including 9 inter-serotype recombinants and 14 strains with unknown sources of recombination. CONCLUSIONS We successfully integrated VP1-CODEHOP and NGS techniques to conduct genomic analysis of serologically untypable enteroviruses.
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Affiliation(s)
- Yeh-Sheng Chien
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Shu-Ting Luo
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
| | - Kuo-Chien Tsao
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Guishan, Taoyuan County Taiwan
- Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Guishan, Taoyuan County Taiwan
| | - Yhu-Chering Huang
- Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Guishan, Taoyuan County Taiwan
| | - Wan-Yu Chung
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County Taiwan
| | - Yi Tan
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee USA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee USA
| | - Min-Shi Lee
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
- National Health Research Institutes, R1-7F, 35 Keyan Road, Zhunan, Miaoli County, 350 Taiwan
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30
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Wang H, Tao K, Leung CY, Hon KL, Yeung CMA, Chen Z, Chan KSP, Leung TF, Chan WYR. Molecular epidemiological study of enterovirus D68 in hospitalised children in Hong Kong in 2014-2015 and their complete coding sequences. BMJ Open Respir Res 2019; 6:e000437. [PMID: 31354952 PMCID: PMC6615781 DOI: 10.1136/bmjresp-2019-000437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 11/16/2022] Open
Abstract
Background Human enterovirus D68 (EV-D68) was first isolated in 1962 and has aroused public concern recently because of a nationwide outbreak among children in 2014–2015 in the USA. The symptoms include fever, runny nose, sneezing, cough and muscle pains. It might be associated with severe respiratory illness in individuals with pre-existing respiratory conditions and its potential association with acute flaccid myelitis is under investigation. In Asia, EV-D68 cases have been reported in several countries. The study We aimed to understand the EV-D68 prevalence and their genetic diversity in Hong Kong children. Methods A total of 10 695 nasopharyngeal aspirate (NPA) samples from hospitalised patients aged <18 years were collected from September 2014 to December 2015 in two regional hospitals. NPAs tested positive for enterovirus/rhinovirus (EV/RV) were selected for genotyping. For those identified as EV-D68, their complete coding sequences (CDSs) were obtained by Sanger sequencing. A maximum-likelihood phylogeny was constructed using all EV-D68 complete coding sequences available in GenBank (n=482). Results 2662/10 695 (24.9%) were tested positive with EV/RV and 882/2662 (33.1%) were selected randomly and subjected to molecular classification. EV-D68 was detected in 15 (1.70%) samples from patients with clinical presentations ranging from wheezing to pneumonia and belonged to subclade B3. Eight CDSs were successfully obtained. A total of 10 amino acid residue polymorphisms were detected in the viral capsid proteins, proteases, ATPase and RNA polymerase. Conclusion B3 subclade was the only subclade found locally. Surveillance of EV-D68 raises public awareness and provides the information to determine the most relevant genotypes for vaccine development.
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Affiliation(s)
- Haichao Wang
- Paediatrics, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong
| | - Kinpong Tao
- Paediatrics, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong.,Chinese University of Hong Kong-University Medical Centre Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, New Territories, Hong Kong
| | - Cheuk Yin Leung
- Paediatrics, Prince of Wales Hospital, New Territories, Hong Kong
| | - Kam Lun Hon
- Paediatrics, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong.,PICU, The Hong Kong Children's Hospital, Hong Kong, Hong Kong
| | - C M Apple Yeung
- Microbiology, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong
| | - Zigui Chen
- Microbiology, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong
| | - K S Paul Chan
- Chinese University of Hong Kong-University Medical Centre Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, New Territories, Hong Kong.,Microbiology, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong
| | - Ting-Fan Leung
- Paediatrics, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong.,Chinese University of Hong Kong-University Medical Centre Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, New Territories, Hong Kong
| | - W Y Renee Chan
- Paediatrics, Chinese University of Hong Kong Faculty of Medicine, New Territories, Hong Kong.,Chinese University of Hong Kong-University Medical Centre Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, New Territories, Hong Kong
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31
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Nath RK, Somasundaram C. Functional Improvement of Upper and Lower Extremity After Decompression and Neurolysis and Nerve Transfer in a Pediatric Patient with Acute Flaccid Myelitis. AMERICAN JOURNAL OF CASE REPORTS 2019; 20:668-673. [PMID: 31073115 PMCID: PMC6523989 DOI: 10.12659/ajcr.915235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Patient: Female, 5 Final Diagnosis: Enterovirus infection Symptoms: Weakness in all 4 limbs Medication: — Clinical Procedure: Nerve decompression • neurolysis and nerve transfer Specialty: Neurosurgery
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Affiliation(s)
- Rahul Kumar Nath
- Department of Surgical Research, Texas Nerve and Paralysis Institute, Houston, TX, USA
| | - Chandra Somasundaram
- Department of Surgical Research, Texas Nerve and Paralysis Institute, Houston, TX, USA
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32
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Dyrdak R, Mastafa M, Hodcroft EB, Neher RA, Albert J. Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing. Virus Evol 2019; 5:vez007. [PMID: 31037220 PMCID: PMC6482344 DOI: 10.1093/ve/vez007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. To investigate diversity, spread, and evolution of EV-D68 we performed near full-length deep sequencing in fifty-four samples obtained in Sweden during the 2014 and 2016 outbreaks. In most samples, intrapatient variability was low and dominated by rare synonymous variants, but three patients showed evidence of dual infections with distinct EV-D68 variants from the same subclade. Interpatient evolution showed a very strong temporal signal, with an evolutionary rate of 0.0039 ± 0.0001 substitutions per site and year. Phylogenetic trees reconstructed from the sequences suggest that EV-D68 was introduced into Stockholm several times during the 2016 outbreak. Putative neutralization targets in the BC and DE loops of the VP1 protein were slightly more diverse within-host and tended to undergo more frequent substitution than other genomic regions. However, evolution in these loops did not appear to have been driven the emergence of the 2016 B3-subclade directly from the 2014 B1-subclade. Instead, the most recent ancestor of both clades was dated to 2009. The study provides a comprehensive description of the intra- and interpatient evolution of EV-D68, including the first report of intrapatient diversity and dual infections. The new data along with publicly available EV-D68 sequences are included in an interactive phylodynamic analysis on nextstrain.org/enterovirus/d68 to facilitate timely EV-D68 tracking in the future.
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Affiliation(s)
- Robert Dyrdak
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Monika Mastafa
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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33
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Shen L, Gong C, Xiang Z, Zhang T, Li M, Li A, Luo M, Huang F. Upsurge of Enterovirus D68 and Circulation of the New Subclade D3 and Subclade B3 in Beijing, China, 2016. Sci Rep 2019; 9:6073. [PMID: 30988475 PMCID: PMC6465342 DOI: 10.1038/s41598-019-42651-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/25/2019] [Indexed: 12/14/2022] Open
Abstract
We conducted a surveillance among acute respiratory tract infection (ARTI) cases to define the epidemiology, clinical characteristics and genetic variations of enterovirus D68 (EV-D68) in Beijing, China from 2015 to 2017. Nasopharyngeal swabs and sputum were collected from 30 sentinel hospitals in Beijing and subjected to EV and EV-D68 detection by real-time PCR. The VP1 gene region and complete genome sequences of EV-D68 positive cases were analyzed. Of 21816 ARTI cases, 619 (2.84%) were EV positive and 42 cases were EV-D68 positive. The detection rates of EV-D68 were 0 (0/6644) in 2015, 0.53% (40/7522) in 2016 and 0.03% (2/7650) in 2017, respectively. Two peaks of EV-D68 infections occurred in late summer and early-winter. Ten cases (23.81%) with upper respiratory tract infection and 32 cases (76.19%) presented with pneumonia, including 3 cases with severe pneumonia. The phylogenetic analysis suggested 15 subclade D3 strains and 27 subclade B3 strains of EV-D68 were circulated in China from 2016 to 2017. A total of 52 amino acid polymorphisms were identified between subclades D1 and D3. These data suggest an upsurge of EV-D68 occurred in Beijing in 2016, the new subclade D3 emerged in 2016 and co-circulated with subclade B3 between 2016 and 2017.
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Affiliation(s)
- Lingyu Shen
- School of Public Health, Capital Medical University, Beijing, 100069, P.R. China
- Institute for immunization and prevention, Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, P.R. China
| | - Cheng Gong
- Institute for immunization and prevention, Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, P.R. China
| | - Zichun Xiang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Foundation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, 100730, P.R. China
| | - Tiegang Zhang
- Institute for immunization and prevention, Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, P.R. China
| | - Maozhong Li
- Institute for immunization and prevention, Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, P.R. China
| | - Aihua Li
- Institute for immunization and prevention, Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, P.R. China
| | - Ming Luo
- School of Public Health, Capital Medical University, Beijing, 100069, P.R. China
| | - Fang Huang
- School of Public Health, Capital Medical University, Beijing, 100069, P.R. China.
- Institute for immunization and prevention, Beijing Municipal Center for Disease Prevention and Control, Beijing, 100013, P.R. China.
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Abstract
Since 2014, acute flaccid myelitis (AFM), a long-recognized condition associated with polioviruses, nonpolio enteroviruses, and various other viral and nonviral causes, has been reemerging globally in epidemic form. This unanticipated reemergence is ironic, given that polioviruses, once the major causes of AFM, are now at the very threshold of global eradication and cannot therefore explain any aspect of AFM reemergence. Instead, the new AFM epidemic has been temporally associated with reemergences of nonpolio enteroviruses such as EV-D68, until recently thought to be an obscure virus of extremely low endemicity. This perspective reviews the enigmatic epidemiologic, virologic, and diagnostic aspects of epidemic AFM reemergence; examines current options for clinical management; discusses future research needs; and suggests that the AFM epidemic offers important clues to mechanisms of viral disease emergence.
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35
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Nikolaidis M, Mimouli K, Kyriakopoulou Z, Tsimpidis M, Tsakogiannis D, Markoulatos P, Amoutzias GD. Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses. Virology 2019; 526:72-80. [DOI: 10.1016/j.virol.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
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36
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Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells. mBio 2018; 9:mBio.01954-18. [PMID: 30327438 PMCID: PMC6191546 DOI: 10.1128/mbio.01954-18] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Since the EV-D68 outbreak during the summer of 2014, evidence of a causal link to a type of limb paralysis (AFM) has been mounting. In this article, we describe a neuronal cell culture model (SH-SY5Y cells) in which a subset of contemporary 2014 outbreak strains of EV-D68 show infectivity in neuronal cells, or neurotropism. We confirmed the difference in neurotropism in vitro using primary human neuron cell cultures and in vivo with a mouse paralysis model. Using the SH-SY5Y cell model, we determined that a barrier to viral entry is at least partly responsible for neurotropism. SH-SY5Y cells may be useful in determining if specific EV-D68 genetic determinants are associated with neuropathogenesis, and replication in this cell line could be used as rapid screening tool for identification of neurotropic EV-D68 strains. This may assist with better understanding of pathogenesis and epidemiology and with the development of potential therapies. Enterovirus D68 (EV-D68) has historically been associated with respiratory illnesses. However, in the summers of 2014 and 2016, EV-D68 outbreaks coincided with a spike in polio-like acute flaccid myelitis/paralysis (AFM/AFP) cases. This raised concerns that EV-D68 could be the causative agent of AFM during these recent outbreaks. To assess the potential neurotropism of EV-D68, we utilized the neuroblastoma-derived neuronal cell line SH-SY5Y as a cell culture model to determine if differential infection is observed for different EV-D68 strains. In contrast to HeLa and A549 cells, which support viral infection of all EV-D68 strains tested, SH-SY5Y cells only supported infection by a subset of contemporary EV-D68 strains, including isolates from the 2014 outbreak. Viral replication and infectivity in SH-SY5Y were assessed using multiple assays: virus production, cytopathic effects, cellular ATP release, and VP1 capsid protein production. Similar differential neurotropism was also observed in differentiated SH-SY5Y cells, primary human neuron cultures, and a mouse paralysis model. Using the SH-SY5Y cell culture model, we determined that barriers to viral binding and entry were at least partly responsible for the differential infectivity phenotype. Transfection of genomic RNA into SH-SY5Y generated virions for all EV-D68 isolates, but only a single round of replication was observed from strains that could not directly infect SH-SY5Y. In addition to supporting virus replication and other functional studies, this cell culture model may help identify the signatures of virulence to confirm epidemiological associations between EV-D68 strains and AFM and allow for the rapid identification and characterization of emerging neurotropic strains.
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37
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Sioofy-Khojine AB, Oikarinen S, Honkanen H, Huhtala H, Lehtonen JP, Briese T, Hyöty H. Molecular epidemiology of enteroviruses in young children at increased risk of type 1 diabetes. PLoS One 2018; 13:e0201959. [PMID: 30192755 PMCID: PMC6128458 DOI: 10.1371/journal.pone.0201959] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/25/2018] [Indexed: 12/15/2022] Open
Abstract
Background Young children are susceptible to enterovirus (EV) infections, which cause significant morbidity in this age group. However, the current knowledge regarding the epidemiology of EVs and the circulating virus strains is mostly based on viruses detected in children with severe diseases leading to contact with the health care system, while the vast reservoir of EVs that circulate in the general population is less characterized. Methodology The present study investigates the types and the prevalence of EVs circulating in the young children of the background population in Georgia, Colorado, and Washington State in the USA, and Germany, Sweden, and Finland in Europe. A total of 4018 stool samples, collected monthly from 300 healthy and non-hospitalized children at the age of 3–18 months in 2005–2009, were analyzed for the presence of EVs using RT-PCR, followed by sequencing of the VP1-2A region of the viral genome to type the EV(s) present. All of the children carried type HLA-DQ2 or -DQ8 alleles associated with type 1 diabetes. Principal findings Altogether 201 children (67%) were found to be EV positive. The prevalence was much lower in Finnish children (26%) than in the children of the other counties combined (75%). Infections increased by age and showed a nadir during the winter months. Children who carried both the HLA-DQ2 and -DQ8 alleles had less infections than children who were homozygous for these alleles. Coxsackieviruses type A were the most frequently detected viruses in all geographical regions. Coxsackievirus type A4, Echovirus type 18, and Echovirus type 25 were shed for longer time periods than the other EV types. Conclusions Compared to prevalence data from symptomatic patients requiring medical attention, this study provides a better view of EVs circulating in young children in the USA and in Europe. The observations may prove useful for the selection of strategies for designing EV vaccines in the future. The study also confirms our previous serological findings suggesting that EV infections are relatively rare in Finland.
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Affiliation(s)
- Amir-Babak Sioofy-Khojine
- Department of Virology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- * E-mail:
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Hanna Honkanen
- Department of Virology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Heini Huhtala
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | - Jussi P. Lehtonen
- Department of Virology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
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38
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Isaacs SR, Kim KW, Cheng JX, Bull RA, Stelzer-Braid S, Luciani F, Rawlinson WD, Craig ME. Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples. Sci Rep 2018; 8:11889. [PMID: 30089864 PMCID: PMC6082906 DOI: 10.1038/s41598-018-30322-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/19/2018] [Indexed: 12/16/2022] Open
Abstract
More than 100 different enterovirus (EV) genotypes infect humans and contribute to substantial morbidity. However, current methods for characterisation of full-length genomes are based on Sanger sequencing of short genomic regions, which are labour-intensive and do not enable comprehensive characterisation of viral populations. Here, we describe a simple and sensitive protocol for the amplification and sequencing of near full-length genomes of human EV species using next generation sequencing. EV genomes were amplified from 89% of samples tested, with Ct values ranging between 15.7 and 39.3. These samples included 7 EV-A genotypes (CVA2, 5–7, 10, 16 and EV71), 19 EV-B genotypes (CVA9, CVB1-6, ECHO3, 4, 6, 7, 9, 11, 16, 18, 25, 29, 30, and EV69), 3 EV-C genotypes (CVA19 and PV2, 3) and 1 EV-D genotype (EV70). We characterised 70 EVs from 58 clinical stool samples and eight reference strains, with a minimum of 100X depth. We found evidence of co-infection in four clinical specimens, each containing two distinct EV genotypes (CVB3/ECHO7, CVB3/ECHO18 and ECHO9/30). Characterisation of the complete genome provided conclusive genotyping of EVs, which can be applied to investigate the intra-host virus evolution of EVs, and allows further identification and investigation of EV outbreaks.
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Affiliation(s)
- Sonia R Isaacs
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
| | - Ki Wook Kim
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
| | - Junipearl X Cheng
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Systems Medicine, Inflammation and Infection Research Centre, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Systems Medicine, Inflammation and Infection Research Centre, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - William D Rawlinson
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW, 2031, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia. .,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia. .,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, 2145, Australia. .,Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW, 2006, Australia.
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Piralla A, Principi N, Ruggiero L, Girello A, Giardina F, De Sando E, Caimmi S, Bianchini S, Marseglia GL, Lunghi G, Baldanti F, Esposito S. Enterovirus-D68 (EV-D68) in pediatric patients with respiratory infection: The circulation of a new B3 clade in Italy. J Clin Virol 2018; 99-100:91-96. [PMID: 29396353 PMCID: PMC7185653 DOI: 10.1016/j.jcv.2018.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/03/2018] [Accepted: 01/11/2018] [Indexed: 11/01/2022]
Abstract
BACKGROUND In recent years, several outbreaks due to Enterovirus D-68 (EV-D68) have been reported, and it was confirmed that the virus can cause upper and lower respiratory tract diseases and be associated with the development of neurological problems. OBJECTIVES The main aim of this research was to study the genetic characteristics of EV-D68 strains that were circulating in Italy identified during an outbreak of an EV-D68 infection that occurred in Italy during the period March-October 2016. STUDY DESIGN A retrospective study of the circulation of different types and subtypes of EV-D68 was performed. Nasopharyngeal swabs were collected from March 2016 through October 2016 in children admitted to the Emergency Room with respiratory diseases. RESULTS Among 390 children, 22 (59.1% males; mean age 47 months) were found to be infected by EV-D68 and most of them were immunocompetent (72.7%). Pneumonia was diagnosed in 12 (54.5%) children. Phylogenetic analysis of the VP1 region showed that all the strains identified in this study belonged to clade B3. Within B3 subclade, the Italian EV-D68 strains were most closely related to strains detected in Southern China in 2015 as well as to strains detected in US and the Netherlands in 2016. CONCLUSIONS These results showed that EV-D68 infections are a common cause of lower respiratory illness in pediatric age. The circulation of one EV-D68 lineage has been proven in Italy and in the European region during 2016. However, further studies are required to investigate whether some strains or lineages may possess a higher affinity for the lower airway or central nervous system.
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Affiliation(s)
- Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Nicola Principi
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milano, Italy
| | - Luca Ruggiero
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milano, Italy
| | - Alessia Girello
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Giardina
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisabetta De Sando
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Università degli Studi di Pavia, Pavia, Italy
| | - Silvia Caimmi
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Università degli Studi di Pavia, Pavia, Italy
| | - Sonia Bianchini
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milano, Italy
| | - Gian Luigi Marseglia
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Università degli Studi di Pavia, Pavia, Italy
| | - Giovanna Lunghi
- Virology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical Surgical, Diagnostic and Pediatric Sciences, Università degli Studi di Pavia, Pavia, Italy
| | - Susanna Esposito
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Piazza Menghini 1, 06129, Perugia, Italy.
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40
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Kaida A, Iritani N, Yamamoto SP, Kanbayashi D, Hirai Y, Togawa M, Amo K, Kohdera U, Nishigaki T, Shiomi M, Asai S, Kageyama T, Kubo H. Distinct genetic clades of enterovirus D68 detected in 2010, 2013, and 2015 in Osaka City, Japan. PLoS One 2017; 12:e0184335. [PMID: 28902862 PMCID: PMC5597212 DOI: 10.1371/journal.pone.0184335] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 08/22/2017] [Indexed: 12/23/2022] Open
Abstract
The first upsurge of enterovirus D68 (EV-D68), a causative agent of acute respiratory infections (ARIs), in Japan was reported in Osaka City in 2010. In this study, which began in 2010, we surveyed EV-D68 in children with ARIs and analyzed sequences of EV-D68 strains detected. Real-time PCR of 19 respiratory viruses or subtypes of viruses, including enterovirus, was performed on 2,215 specimens from ARI patients (<10 years of age) collected between November 2010 and December 2015 in Osaka City, Japan. EV-D68 was identified in 18 enterovirus-positive specimens (n = 4 in 2013, n = 1 in 2014, and n = 13 in 2015) by analysis of viral protein 1 (VP1) or VP4 sequences, followed by a BLAST search for similar sequences. All EV-D68 strains were detected between June and October (summer to autumn), except for one strain detected in 2014. A phylogenetic analysis of available VP1 sequences revealed that the Osaka strains detected in 2010, 2013, and 2015 belonged to distinct clusters (Clades C, A, and B [Subclade B3], respectively). Comparison of the 5' untranslated regions of these viruses showed that Osaka strains in Clades A, B (Subclade B3), and C commonly had deletions at nucleotide positions 681-703 corresponding to the prototype Fermon strain. Clades B and C had deletions from nucleotide positions 713-724. Since the EV-D68 epidemic in 2010, EV-D68 re-emerged in Osaka City, Japan, in 2013 and 2015. Results of this study indicate that distinct clades of EV-D68 contributed to re-emergences of this virus in 2010, 2013, and 2015 in this limited region.
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Affiliation(s)
- Atsushi Kaida
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
- * E-mail:
| | - Nobuhiro Iritani
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Seiji P. Yamamoto
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Daiki Kanbayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yuki Hirai
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | | | - Kiyoko Amo
- Osaka City General Hospital, Osaka, Japan
| | | | | | | | | | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideyuki Kubo
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
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Revealing enterovirus infection in chronic human disorders: An integrated diagnostic approach. Sci Rep 2017; 7:5013. [PMID: 28694527 PMCID: PMC5504018 DOI: 10.1038/s41598-017-04993-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/09/2017] [Indexed: 01/10/2023] Open
Abstract
Enteroviruses (EVs) causing persisting infection are characterized by minimal replication and genetic changes. Typing of these agents may complement disease assessment and shed light on pathogenesis. Here we report an integrated approach for EV detection in human samples that is based on pre-enrichment of virus in cell culture before search for the viral genome and viral antigens. Cases of post-polio syndrome, type 1 diabetes, and chronic cardiomyopathy were investigated. As tissue-based approaches require invasive procedures, information was mainly gleaned from virus in blood. Molecular assays targeting conserved genome regions of all EV types (5'UTR, 2 C, 3Dpol) were employed. As compared to direct assays of plasma or leukocytes, the EV detection rate was significantly enhanced by co-culture of leukocytes with cell lines prior to molecular and immunologic tests. Results of RT-PCR and sequencing were confirmed by staining cell cultures with a panel of EV-specific antibodies. Sequence and phylogenetic analysis showed that EVs of the C species (polioviruses) were associated with the post-polio syndrome, while members of the B species were found in type 1 diabetes and cardiomyopathy. The procedure may be used for investigating the possible association of different EVs with a variety of chronic neurologic, endocrine, and cardiac disorders.
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42
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Ny NTH, Anh NT, Hang VTT, Nguyet LA, Thanh TT, Ha DQ, Minh NNQ, Ha DLA, McBride A, Tuan HM, Baker S, Tam PTT, Phuc TM, Huong DT, Loi TQ, Vu NTA, Hung NV, Minh TTT, Xang NV, Dong N, Nghia HDT, Chau NVV, Thwaites G, van Doorn HR, Anscombe C, Le Van T. Enterovirus D68 in Viet Nam (2009-2015). Wellcome Open Res 2017. [PMID: 28852711 DOI: 10.12688/wellcomeopenres.11558.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Since 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, but especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015. METHODS Enterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam between 2009 and 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively. RESULTS EV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 - 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E -3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008. CONCLUSIONS We have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.
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Affiliation(s)
- Nguyen Thi Han Ny
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Ho Chi Minh City University of Science, Ho Chi Minh City, Vietnam
| | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ty Hang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Lam Anh Nguyet
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Do Quang Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Do Lien Anh Ha
- Murdoch Children's Research Institute, Melbourne, Australia
| | - Angela McBride
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Manh Tuan
- Children's Hospital 2, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Tran My Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Dang Thao Huong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Quoc Loi
- Dong Thap General Hospital, Ban Me Thuot City, Vietnam
| | | | | | | | | | - Nguyen Dong
- Khanh Hoa General Hospital, Nha Trang City, Vietnam
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Pham Ngoc Thach University, Ho Chi Minh City, Vietnam
| | | | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Tan Le Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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43
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Ny NTH, Anh NT, Hang VTT, Nguyet LA, Thanh TT, Ha DQ, Minh NNQ, Ha DLA, McBride A, Tuan HM, Baker S, Tam PTT, Phuc TM, Huong DT, Loi TQ, Vu NTA, Hung NV, Minh TTT, Xang NV, Dong N, Nghia HDT, Chau NVV, Thwaites G, van Doorn HR, Anscombe C, Le Van T. Enterovirus D68 in Viet Nam (2009-2015). Wellcome Open Res 2017; 2:41. [PMID: 28852711 PMCID: PMC5553084 DOI: 10.12688/wellcomeopenres.11558.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2017] [Indexed: 11/30/2022] Open
Abstract
Background: Since 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015. Methods: Enterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam 2009 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively. Results: EV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 – 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E
-3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008. Conclusions: We have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.
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Affiliation(s)
- Nguyen Thi Han Ny
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Ho Chi Minh City University of Science, Ho Chi Minh City, Vietnam
| | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ty Hang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Lam Anh Nguyet
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Do Quang Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Do Lien Anh Ha
- Murdoch Children's Research Institute, Melbourne, Australia
| | - Angela McBride
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Manh Tuan
- Children's Hospital 2, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Tran My Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Dang Thao Huong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Quoc Loi
- Dong Thap General Hospital, Ban Me Thuot City, Vietnam
| | | | | | | | | | - Nguyen Dong
- Khanh Hoa General Hospital, Nha Trang City, Vietnam
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Pham Ngoc Thach University, Ho Chi Minh City, Vietnam
| | | | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Tan Le Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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44
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First Report of a Fatal Case Associated with EV-D68 Infection in Hong Kong and Emergence of an Interclade Recombinant in China Revealed by Genome Analysis. Int J Mol Sci 2017; 18:ijms18051065. [PMID: 28509856 PMCID: PMC5454976 DOI: 10.3390/ijms18051065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/04/2017] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
A fatal case associated with enterovirus D68 (EV-D68) infection affecting a 10-year-old boy was reported in Hong Kong in 2014. To examine if a new strain has emerged in Hong Kong, we sequenced the partial genome of the EV-D68 strain identified from the fatal case and the complete VP1, and partial 5′UTR and 2C sequences of nine additional EV-D68 strains isolated from patients in Hong Kong. Sequence analysis indicated that a cluster of strains including the previously recognized A2 strains should belong to a separate clade, clade D, which is further divided into subclades D1 and D2. Among the 10 EV-D68 strains, 7 (including the fatal case) belonged to the previously described, newly emerged subclade B3, 2 belonged to subclade B1, and 1 belonged to subclade D1. Three EV-D68 strains, each from subclades B1, B3, and D1, were selected for complete genome sequencing and recombination analysis. While no evidence of recombination was noted among local strains, interclade recombination was identified in subclade D2 strains detected in mainland China in 2008 with VP2 acquired from clade A. This study supports the reclassification of subclade A2 into clade D1, and demonstrates interclade recombination between clades A and D2 in EV-D68 strains from China.
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45
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Nasal Infection of Enterovirus D68 Leading to Lower Respiratory Tract Pathogenesis in Ferrets (Mustela putorius furo). Viruses 2017; 9:v9050104. [PMID: 28489053 PMCID: PMC5454417 DOI: 10.3390/v9050104] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/30/2017] [Accepted: 05/05/2017] [Indexed: 12/25/2022] Open
Abstract
Data from EV-D68-infected patients demonstrate that pathological changes in the lower respiratory tract are principally characterized by severe respiratory illness in children and acute flaccid myelitis. However, lack of a suitable animal model for EV-D68 infection has limited the study on the pathogenesis of this critical pathogen, and the development of a vaccine. Ferrets have been widely used to evaluate respiratory virus infections. In the current study, we used EV-D68-infected ferrets as a potential animal to identify impersonal indices, involving clinical features and histopathological changes in the upper and lower respiratory tract (URT and LRT). The research results demonstrate that the EV-D68 virus leads to minimal clinical symptoms in ferrets. According to the viral load detection in the feces, nasal, and respiratory tracts, the infection and shedding of EV-D68 in the ferret model was confirmed, and these results were supported by the EV-D68 VP1 immunofluorescence confocal imaging with α2,6-linked sialic acid (SA) in lung tissues. Furthermore, we detected the inflammatory cytokine/chemokine expression level, which implied high expression levels of interleukin (IL)-1a, IL-8, IL-5, IL-12, IL-13, and IL-17a in the lungs. These data indicate that systemic observation of responses following infection with EV-D68 in ferrets could be used as a model for EV-D68 infection and pathogenesis.
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46
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Abstract
BACKGROUND Enterovirus D68 (EV-D68) has been sporadically reported as a cause of respiratory tract infections. In 2014, an international outbreak of EV-D68 occurred and caused severe respiratory disease in the pediatric population. METHODS A retrospective chart review was performed of children admitted to Children's Mercy Hospital from August 1, 2014, to September 15, 2014, with positive multiplex polymerase chain reaction testing for EV/rhinovirus (RV). Specimens were subsequently tested for EV-D68, and clinical data were obtained from the medical records. Patients with EV-D68 were compared with children presenting simultaneously with other EV/RV. RESULTS Of 542 eligible specimens, children with EV-D68 were significantly older than children with other EV/RV (4.6 vs. 2.2 years, P < 0.001). Children with EV-D68 were more likely to have a history of asthma (38.6% vs. 30.0%, P = 0.04) or recurrent wheezing (22.1% vs. 14.8%, P = 0.04). EV-D68-positive children more commonly received supplemental oxygen (86.7% vs. 65.0%, P < 0.001), albuterol (91.2% vs. 65.5%, P < 0.001) and corticosteroids (82.9% vs. 58.6%, P < 0.001). Age ≥5 years was an independent risk factor for intensive care unit management in EV-D68-infected children. Children with a history of asthma or recurrent wheezing and EV-D68 received supplemental oxygen (92.7% vs. 82.4%, P = 0.007) and magnesium (42.7% vs. 29.7%, P = 0.03) at higher rates and more continuous albuterol (3 vs. 2 hours, P = 0.03) than those with other EV/RV. CONCLUSIONS EV-D68 causes severe disease in the pediatric population, particularly in children with a history of asthma or recurrent wheezing. EV-D68-positive children are more likely to require therapy for refractory bronchospasm and may need intensive care unit- level care.
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47
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Patel MC, Wang W, Pletneva LM, Rajagopala SV, Tan Y, Hartert TV, Boukhvalova MS, Vogel SN, Das SR, Blanco JCG. Enterovirus D-68 Infection, Prophylaxis, and Vaccination in a Novel Permissive Animal Model, the Cotton Rat (Sigmodon hispidus). PLoS One 2016; 11:e0166336. [PMID: 27814404 PMCID: PMC5096705 DOI: 10.1371/journal.pone.0166336] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/26/2016] [Indexed: 12/17/2022] Open
Abstract
In recent years, there has been a significant increase in detection of Enterovirus D-68 (EV-D68) among patients with severe respiratory infections worldwide. EV-D68 is now recognized as a re-emerging pathogen; however, due to lack of a permissive animal model for EV-D68, a comprehensive understanding of the pathogenesis and immune response against EV-D68 has been hampered. Recently, it was shown that EV-D68 has a strong affinity for α2,6-linked sialic acids (SAs) and we have shown previously that α2,6-linked SAs are abundantly present in the respiratory tract of cotton rats (Sigmodon hispidus). Thus, we hypothesized that cotton rats could be a potential model for EV-D68 infection. Here, we evaluated the ability of two recently isolated EV-D68 strains (VANBT/1 and MO/14/49), along with the historical prototype Fermon strain (ATCC), to infect cotton rats. We found that cotton rats are permissive to EV-D68 infection without virus adaptation. The different strains of EV-D68 showed variable infection profiles and the ability to produce neutralizing antibody (NA) upon intranasal infection or intramuscular immunization. Infection with the VANBT/1 resulted in significant induction of pulmonary cytokine gene expression and lung pathology. Intramuscular immunization with live VANBT/1 or MO/14/49 induced strong homologous antibody responses, but a moderate heterologous NA response. We showed that passive prophylactic administration of serum with high content of NA against VANBT/1 resulted in an efficient antiviral therapy. VANBT/1-immunized animals showed complete protection from VANBT/1 challenge, but induced strong pulmonary Th1 and Th2 cytokine responses and enhanced lung pathology, indicating the generation of exacerbated immune response by immunization. In conclusion, our data illustrate that the cotton rat is a powerful animal model that provides an experimental platform to investigate pathogenesis, immune response, anti-viral therapies and vaccines against EV-D68 infection.
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Affiliation(s)
- Mira C. Patel
- Sigmovir Biosystems Inc., Rockville, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
| | - Wei Wang
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Seesandra V. Rajagopala
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Yi Tan
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Tina V. Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | | | - Stefanie N. Vogel
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
| | - Suman R. Das
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail: (JCGB); (SRD)
| | - Jorge C. G. Blanco
- Sigmovir Biosystems Inc., Rockville, Maryland, United States of America
- * E-mail: (JCGB); (SRD)
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48
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Identification and Whole-Genome Sequencing of Four Enterovirus D68 Strains in Southern China in Late 2015. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01014-16. [PMID: 27660790 PMCID: PMC5034141 DOI: 10.1128/genomea.01014-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Four enterovirus D68 (EV-D68) strains from four children with influenza-like illness were identified in Shenzhen, southern China, in late 2015. Here, we announce the availability of these viral genomes in GenBank. The genomic sequences of these EV-D68 strains showed the closest phylogenetic relationship to strains from northern China.
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49
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Gong YN, Yang SL, Shih SR, Huang YC, Chang PY, Huang CG, Kao KC, Hu HC, Liu YC, Tsao KC. Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis. Medicine (Baltimore) 2016; 95:e4416. [PMID: 27495059 PMCID: PMC4979813 DOI: 10.1097/md.0000000000004416] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Human enterovirus D68 (EV-D68) was first reported in the United States in 1962; thereafter, a few cases were reported from 1970 to 2005, but 2 outbreaks occurred in the Philippines (2008) and the United States (2014). However, little is known regarding the molecular evolution of this globally reemerging virus due to a lack of whole-genome sequences and analyses. Here, all publically available sequences including 147 full and 1248 partial genomes from GenBank were collected and compared at the clade and subclade level; 11 whole genomes isolated in Taiwan (TW) in 2014 were also added to the database. Phylogenetic trees were constructed to identify a new subclade, B3, and represent clade circulations among strains. Nucleotide sequence identities of the VP1 gene were 94% to 95% based on a comparison of subclade B3 to B1 and B2 and 87% to 91% when comparing A, C, and D. The patterns of clade circulation need to be clarified to improve global monitoring of EV-D68, even though this virus showed lower diversity among clades compared with the common enterovirus EV-71. Notably, severe cases isolated from Taiwan and China in 2014 were found in subclade B3. One severe case from Taiwan occurred in a female patient with underlying angioimmunoblastic T-cell lymphoma, from whom a bronchoalveolar lavage specimen was obtained. Although host factors play a key role in disease severity, we cannot exclude the possibility that EV-D68 may trigger clinical symptoms or death. To further investigate the genetic diversity of EV-D68, we reported 34 amino acid (aa) polymorphisms identified by comparing subclade B3 to B1 and B2. Clade D strains had a 1-aa deletion and a 2-aa insertion in the VP1 gene, and 1 of our TW/2014 strains had a shorter deletion in the 5' untranslated region than a previously reported deletion. In summary, a new subclade, genetic indels, and polymorphisms in global strains were discovered elucidating evolutionary and epidemiological trends of EV-D68, and 11 genomes were added to the database. Virus variants may contribute to disease severity and clinical manifestations, and further studies are needed to investigate the associations between genetic diversity and clinical outcomes.
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Affiliation(s)
- Yu-Nong Gong
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
| | - Shu-Li Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
- Department of Medical Biotechnology and Laboratory Science
| | - Shin-Ru Shih
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
- Department of Medical Biotechnology and Laboratory Science
- Research Center for Emerging Viral Infections, Chang Gung University
| | - Yhu-Chering Huang
- Department of Pediatrics, Linkou Chang Gung Memorial Hospital
- College of Medicine, Chang Gung University
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
- Department of Medical Biotechnology and Laboratory Science
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
- Department of Medical Biotechnology and Laboratory Science
- Research Center for Emerging Viral Infections, Chang Gung University
| | - Kuo-Chin Kao
- Department of Respiratory Therapy
- Department of Pulmonary and Critical Care Medicine, Linkou Chang Gung Memorial Hospital
- Department of Respiratory Therapy
- Department of Pulmonary and Critical Care Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Han-Chung Hu
- Department of Respiratory Therapy
- Department of Pulmonary and Critical Care Medicine, Linkou Chang Gung Memorial Hospital
- Department of Respiratory Therapy
- Department of Pulmonary and Critical Care Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Chun Liu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
| | - Kuo-Chien Tsao
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
- Department of Medical Biotechnology and Laboratory Science
- Research Center for Emerging Viral Infections, Chang Gung University
- Correspondence: Kuo-ChienTsao, Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan (e-mail: )
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50
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Lau SKP, Yip CCY, Zhao PSH, Chow WN, To KKW, Wu AKL, Yuen KY, Woo PCY. Enterovirus D68 Infections Associated with Severe Respiratory Illness in Elderly Patients and Emergence of a Novel Clade in Hong Kong. Sci Rep 2016; 6:25147. [PMID: 27121085 PMCID: PMC4848506 DOI: 10.1038/srep25147] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
Despite the recent emergence of enterovirus D68 (EV-D68), its clinical impact on adult population is less well defined. To better define the epidemiology of EV-D68, 6,800 nasopharyngeal aspirates (NPAs) from 2010–2014 were subject to EV-D68 detection by RT-PCR and sequencing of 5′UTR and partial VP1. EV-D68 was detected in 30 (0.44%) NPAs from 22 children and 8 adults/elderlies. Sixteen patients (including five elderly) (53%) had pneumonia and 13 (43%) patients were complicated by small airway disease exacerbation. Phylogenetic analysis of VP1, 2C and 3D regions showed four distinct lineages of EV-D68, clade A1, A2, B1 and B3, with adults/elderlies exclusively infected by clade A2. The potentially new clade, B3, has emerged in 2014, while strains closely related to recently emerged B1 strains in the United States were also detected as early as 2011 in Hong Kong. The four lineages possessed distinct aa sequence patterns in BC and DE loops. Amino acid residues 97 and 140, within BC and DE-surface loops of VP1 respectively, were under potential positive selection. EV-D68 infections in Hong Kong usually peak in spring/summer, though with a delayed autumn/winter peak in 2011. This report suggests that EV-D68 may cause severe respiratory illness in adults/elderlies with underlying co-morbidities.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Pyrear Su-Hui Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kelvin K W To
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Alan K L Wu
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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