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Vink E, Banda L, Amoah AS, Kasenda S, Read JM, Jewell C, Denis B, Mwale AC, Crampin A, Anscombe C, Menyere M, Ho A. Prevalence of Endemic Respiratory Viruses During the COVID-19 Pandemic in Urban and Rural Malawi. Open Forum Infect Dis 2024; 11:ofad643. [PMID: 38312213 PMCID: PMC10836885 DOI: 10.1093/ofid/ofad643] [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: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 02/06/2024] Open
Abstract
Background We investigated endemic respiratory virus circulation patterns in Malawi, where no lockdown was imposed, during the COVID-19 pandemic. Methods Within a prospective household cohort in urban and rural Malawi, adult participants provided upper respiratory tract (URT) samples at 4 time points between February 2021 and April 2022. Polymerase chain reaction (PCR) was performed for SARS-CoV-2, influenza, and other endemic respiratory viruses. Results 1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) samples were PCR- positive for >1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most common. No influenza A virus was detected. Influenza B and respiratory syncytial virus (RSV) were rare. Higher virus positivity were detected in the rural setting and at earlier time points. Coinfections were infrequent. Conclusions Endemic respiratory viruses circulated in the community in Malawi during the pandemic, though influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts.
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Affiliation(s)
- Elen Vink
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Louis Banda
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
| | - Abena S Amoah
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
- Department of Population Health, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Leiden University Medical Center, Leiden, the Netherlands
| | - Stephen Kasenda
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
| | - Jonathan M Read
- Centre for Health Information Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Chris Jewell
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - Amelia Crampin
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
- Department of Population Health, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Catherine Anscombe
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
- Liverpool School of Tropical Medicine, University of Liverpool, Liverpool, UK
| | - Mavis Menyere
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Li Y, Wang X, Xu R, Wang T, Zhang D, Qian W. Establishment of RT-RPA-Cas12a assay for rapid and sensitive detection of human rhinovirus B. BMC Microbiol 2023; 23:333. [PMID: 37951882 PMCID: PMC10640725 DOI: 10.1186/s12866-023-03096-1] [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: 02/25/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023] Open
Abstract
Human rhinovirus B (HRV-B) is a major human viral pathogen that can be responsible for various kinds of infections. Due to the health risks associated with HRV-B, it is therefore crucial to explore a rapid, specific, and sensitive method for surveillance. Herein, we exploited a novel detection method for HRV-B by combining reverse-transcription recombinase polymerase amplification (RT-RPA) of nucleic acids isothermal amplification and the trans-cleavage activity of Cas12a. Our RT-RPA-Cas12a-based fluorescent assay can be completed within 35-45 min and obtain a lower detection threshold to 0.5 copies/µL of target RNA. Meanwhile, crRNA sequences without a specific protospacer adjacent motif can effectively activate the trans-cleavage activity of Cas12a. Moreover, our RT-RPA-Cas12a-based fluorescent method was examined using 30 clinical samples, and exhibited high accuracy with positive and negative predictive agreement of 90% and 100%, respectively. Taken together, a novel promising, rapid and effective RT-RPA-Cas12a-based detection method was explored and shows promising potential for on-site HRV-B infection in resource-limited settings.
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Affiliation(s)
- Yongdong Li
- Ningbo Key Laboratory of Virus Research, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, P. R. China
| | - Xuefei Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Rong Xu
- Ningbo Key Laboratory of Virus Research, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, P. R. China
| | - Ting Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Dandan Zhang
- Ningbo Key Laboratory of Virus Research, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, P. R. China.
| | - Weidong Qian
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China.
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3
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Morais-Armas S, Medina-Suárez S, Machín F. Effect of carrier yeast RNAs in the detection of SARS-CoV-2 by RT-LAMP. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000979. [PMID: 37799204 PMCID: PMC10550381 DOI: 10.17912/micropub.biology.000979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has underscored the need for rapid and accurate diagnostic methods. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) has emerged as a promising molecular tool in least developed countries due to its simplicity, speed, and sensitivity. Nevertheless, reliable SARS-CoV-2 detection can be challenged by the chain custody of the samples. In this context, carrier RNA can act as a preservative. In this study, we explored the potential of yeast total and transference RNA (tRNA) in the SARS-CoV-2 RT-LAMP. We have found that most optimal conditions are reached with 1 μg/μL tRNA in the RT-LAMP reaction.
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Affiliation(s)
- Samantha Morais-Armas
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, San Cristóbal de La Laguna, Canary Islands, Spain
| | - Sara Medina-Suárez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, San Cristóbal de La Laguna, Canary Islands, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, San Cristóbal de La Laguna, Canary Islands, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Canary Islands, Spain
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4
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Cong S, Wang C, Wei T, Xie Z, Huang Y, Tan J, Chen A, Ma F, Zheng L. Human metapneumovirus in hospitalized children with acute respiratory tract infections in Beijing, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105386. [PMID: 36372116 DOI: 10.1016/j.meegid.2022.105386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND This study aims to described the epidemiology and genotypic diversity of Human metapneumovirus (HMPV) and the impact of SARS-CoV-2 on the prevalence of HMPV in hospitalized children with Acute respiratory tract infections (ARTIs) in Beijing, China. METHODS From April 2018 to March 2019 and from September 2020 to August 2021, nasopharyngeal aspirates (NPAs) from hospitalized children with ARTIs in Beijing were collected and subjected to real-time polymerase chain reaction tests for HMPV. Then genotyping, detection of 15 common respiratory viruses and clinical characteristics were analyzed on HMPV positive samples. RESULTS 7.9% (124/1572) enrolled pediatric patients were identified as having HMPV infection, and the majority of children under the age of 5 (78.2%, 92/124), From April 2018 to March 2019. The detection rate of HMPV in spring and winter is significantly higher than that in summer and autumn. The co-infection rate were 37.1% (46/124), the most common co-infected virus were parainfluenza virus type 3 (HPIV-3). The main diagnosis of HMPV infection was pneumonia (92.7%,115/124), most patient have cough and fever. Of 78 HMPV-positive specimens, A2b (82.1%,64/78) were the main epidemic subtypes. Hospitalized children with HMPV genotype A infection had a higher viral load compared to genotype B. During the COVID-19 outbreak, Among 232 samples, only 4 cases were HMPV-positive. After statistical test, the detection rate of HMPV during the COVID-19 pandemic has decreased significantly compared with that before the epidemic (p = 0.001). CONCLUSIONS HMPV is an important cause of ARTIs in children under 5 years old. The epidemic peak is generally in winter and spring, and the A2b subtype is the most common. However, under the prevention and control of the COVID-19 pandemic, the HMPV infection of hospitalized children with ARTIs has decreased significantly.
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Affiliation(s)
- Shanshan Cong
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China; Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Chao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Tianli Wei
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhiping Xie
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yiman Huang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jingjing Tan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China; Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Aijun Chen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Fenlian Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.
| | - Lishu Zheng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.
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Ivaska LE, Silvoniemi A, Mikola E, Puhakka T, Waris M, Vuorinen T, Jartti T. Herpesvirus infections in adenoids in patients with chronic adenotonsillar disease. J Med Virol 2022; 94:4470-4477. [PMID: 35488185 PMCID: PMC9545566 DOI: 10.1002/jmv.27818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/18/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022]
Abstract
Adenoids and tonsils have gained interest as a new in vivo model to study local immune functions and virus reservoirs. Especially herpesviruses are interesting because their prevalence and persistence in local lymphoid tissue are incompletely known. Our aim was to study herpesvirus and common respiratory virus infections in nonacutely ill adenotonsillar surgery patients. Adenoid and/or palatine tonsil tissue and nasopharyngeal aspirate (NPA) samples were collected from elective adenoidectomy (n = 45) and adenotonsillectomy (n = 44) patients (median age: 5, range: 1–20). Real‐time polymerase chain reaction was used to detect 22 distinct viruses from collected samples. The overall prevalence of herpesviruses was 89% and respiratory viruses 94%. Human herpesviruses 6 (HHV6), 7 (HHV7), and Epstein–Barr virus (EBV) were found, respectively, in adenoids (33%, 26%, 25%), tonsils (45%, 52%, 23%), and NPA (46%, 38%, 25%). Copy numbers of the HHV6 and HHV7 genome were significantly higher in tonsils than in adenoids. Patients with intra‐adenoid HHV6 were younger than those without. Detection rates of EBV and HHV7 showed agreement between corresponding sample types. This study shows that adenoid and tonsil tissues commonly harbor human herpes‐ and respiratory viruses, and it shows the differences in virus findings between sample types.
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Affiliation(s)
- Lotta E Ivaska
- Department of Otorhinolaryngology - Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland
| | - Antti Silvoniemi
- Department of Otorhinolaryngology - Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland
| | - Emilia Mikola
- Department of Otorhinolaryngology - Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland.,Department of Otorhinolaryngology, Satakunta Central Hospital, Pori, Finland
| | - Tuomo Puhakka
- Department of Otorhinolaryngology - Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland
| | - Matti Waris
- Institute of Biomedicine, University of Turku, Turku, Finland.,Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Tytti Vuorinen
- Institute of Biomedicine, University of Turku, Turku, Finland.,Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Tuomas Jartti
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland.,PEDEGO Research Unit, Medical Research Center, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
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Hietanen E, Koivu MKA, Susi P. Cytolytic Properties and Genome Analysis of Rigvir ® Oncolytic Virotherapy Virus and Other Echovirus 7 Isolates. Viruses 2022; 14:525. [PMID: 35336934 PMCID: PMC8949920 DOI: 10.3390/v14030525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 01/19/2023] Open
Abstract
Rigvir® is a cell-adapted, oncolytic virotherapy enterovirus, which derives from an echovirus 7 (E7) isolate. While it is claimed that Rigvir® causes cytolytic infection in several cancer cell lines, there is little molecular evidence for its oncolytic and oncotropic potential. Previously, we genome-sequenced Rigvir® and five echovirus 7 isolates, and those sequences are further analyzed in this paper. A phylogenetic analysis of the full-length data suggested that Rigvir® was most distant from the other E7 isolates used in this study, placing Rigvir® in its own clade at the root of the phylogeny. Rigvir® contained nine unique mutations in the viral capsid proteins VP1-VP4 across the whole data set, with a structural analysis showing six of the mutations concerning residues with surface exposure on the cytoplasmic side of the viral capsid. One of these mutations, E/Q/N162G, was located in the region that forms the contact interface between decay-accelerating factor (DAF) and E7. Rigvir® and five other isolates were also subjected to cell infectivity assays performed on eight different cell lines. The used cell lines contained both cancer and non-cancer cell lines for observing Rigvir®'s claimed properties of being both oncolytic and oncotropic. Infectivity assays showed that Rigvir® had no discernable difference in the viruses' oncolytic effect when compared to the Wallace prototype or the four other E7 isolates. Rigvir® was also seen infecting non-cancer cell lines, bringing its claimed effect of being oncotropic into question. Thus, we conclude that Rigvir®'s claim of being an effective treatment against multiple different cancers is not warranted under the evidence presented here. Bioinformatic analyses do not reveal a clear mechanism that could elucidate Rigvir®'s function at a molecular level, and cell infectivity tests do not show a discernable difference in either the oncolytic or oncotropic effect between Rigvir® and other clinical E7 isolates used in the study.
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Affiliation(s)
- Eero Hietanen
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (E.H.); (M.K.A.K.)
- Turku Doctoral Programme of Molecular Medicine, University of Turku, 20520 Turku, Finland
| | - Marika K. A. Koivu
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (E.H.); (M.K.A.K.)
- Turku Doctoral Programme of Molecular Medicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku, 20520 Turku, Finland
| | - Petri Susi
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (E.H.); (M.K.A.K.)
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Huang Y, Wang C, Ma F, Guo Q, Yao L, Chen A, Luo X, Zheng L. Human adenoviruses in paediatric patients with respiratory tract infections in Beijing, China. Virol J 2021; 18:191. [PMID: 34556127 PMCID: PMC8460180 DOI: 10.1186/s12985-021-01661-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/14/2021] [Indexed: 02/07/2023] Open
Abstract
Background Human adenoviruse (HAdV) is a major pathogen of paediatric respiratory tract infections (RTIs). Mutation or recombination of HAdV genes may cause changes in its pathogenicity and transmission. We described the epidemiology and genotypic diversity of HAdV in hospitalized children with RTIs in Beijing, China. Methods Nasopharyngeal aspirates were collected from hospitalized children with RTIs from April 2018 to March 2019. HAdVs were detected by a quantitative real-time PCR, and the hexon gene was used for phylogenetic analysis. Results Among 1572 samples, 90 (5.72%) were HAdV-positive. The HAdV detection rate was highest in November and July. Among HAdV-positive children, 61.11% (55/90) were co-infected with other respiratory viruses, the most common of which were human respiratory syncytial virus and human rhinovirus. The main diagnosis was bronchopneumonia, most patient have cough and fever. Children with a high viral load were more likely to have a high fever (P = 0.041) and elevated WBC count (P = 0.000). Of 55 HAdV-positive specimens, HAdV-B (63.64%), HAdV-C (27.27%), and HAdV-E (9.09%) were main epidemic species. Phylogenetic analysis indicated that hexon sequences of three samples were on the same branch with the recombinant HAdV strain (CBJ113), which was circulating in Beijing since 2016. Conclusion The HAdV-B3 and HAdV-B7 are the main epidemic strains in Beijing, and the recombinant HAdV-C strain CBJ113 has formed an epidemic trend. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01661-6.
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Affiliation(s)
- Yiman Huang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Chao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Fenlian Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Qiong Guo
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Lihong Yao
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Aijun Chen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Xiaoyi Luo
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Lishu Zheng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.
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Ivaska LE, Silvoniemi A, Palomares O, Turunen R, Waris M, Mikola E, Puhakka T, Söderlund‐Venermo M, Akdis M, Akdis CA, Jartti T. Persistent human bocavirus 1 infection and tonsillar immune responses. Clin Transl Allergy 2021; 11:e12030. [PMID: 34435757 PMCID: PMC8459348 DOI: 10.1002/clt2.12030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/19/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Persistent human bocavirus 1 (HBoV1) infection is a common finding in patients suffering from chronic tonsillar disease. However, the associations between HBoV1 infection and specific immune reactions are not completely known. We aimed to compare in vivo expression of T-cell cytokines, transcription factors, and type I/III interferons in human tonsils between HBoV1-positive and -negative tonsillectomy patients. METHODS Tonsil tissue samples, nasopharyngeal aspirate (NPA), and serum samples were obtained from 143 immunocompetent adult and child tonsillectomy patients. HBoV1 and 14 other respiratory viruses were detected in NPAs and tonsil tissues by polymerase chain reaction (PCR). Serology and semi-quantitative PCR were used for diagnosing HBoV1 infections. Expression of 14 cytokines and transcription factors (IFN-α, IFN-β, IFN-γ, IL-10, IL-13, IL-17, IL-28, IL-29, IL-37, TGF-β, FOXP3, GATA3, RORC2, Tbet) was analyzed by quantitative reverse-transcription (RT)-PCR in tonsil tissues. RESULTS HBoV1 was detected by PCR in NPA and tonsils from 25 (17%) study patients. Serology results indicated prior nonacute infections in 81% of cases. Tonsillar cytokine responses were affected by HBoV1 infection. The suppression of two transcription factors, RORC2 and FOXP3, was associated with HBoV1 infection (p < 0.05). Furthermore, intratonsillar HBoV1-DNA loads correlated negatively with IFN-λ family cytokines and IL-13. CONCLUSIONS Our study shows distinctively decreased T-helper17 and T-regulatory type immune responses in local lymphoid tissue in HBoV1-positive tonsillectomy patients. HBoV1 may act as a suppressive immune modulator.
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Affiliation(s)
- Lotta E. Ivaska
- Department of Otorhinolaryngology – Head and Neck SurgeryTurku University Hospital and University of TurkuTurkuFinland
| | - Antti Silvoniemi
- Department of Otorhinolaryngology – Head and Neck SurgeryTurku University Hospital and University of TurkuTurkuFinland
| | - Oscar Palomares
- Swiss Institute of Allergy and Asthma ResearchUniversity of ZürichDavosSwitzerland
- Christine Kühne‐Center for Allergy Research and EducationDavosSwitzerland
- Department of Biochemistry and Molecular BiologySchool of ChemistryComplutense University of MadridMadridSpain
| | - Riitta Turunen
- Department of Pediatrics and Adolescent MedicineTurku University Hospital and University of TurkuTurkuFinland
- Children's HospitalHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Matti Waris
- Clinical MicrobiologyTurku University HospitalTurkuFinland
- Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Emilia Mikola
- Department of Otorhinolaryngology – Head and Neck SurgeryTurku University Hospital and University of TurkuTurkuFinland
- Department of OtorhinolaryngologySatakunta Central HospitalPoriFinland
| | - Tuomo Puhakka
- Department of Otorhinolaryngology – Head and Neck SurgeryTurku University Hospital and University of TurkuTurkuFinland
- Department of OtorhinolaryngologySatakunta Central HospitalPoriFinland
| | | | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma ResearchUniversity of ZürichDavosSwitzerland
- Christine Kühne‐Center for Allergy Research and EducationDavosSwitzerland
| | - Cezmi A. Akdis
- Swiss Institute of Allergy and Asthma ResearchUniversity of ZürichDavosSwitzerland
- Christine Kühne‐Center for Allergy Research and EducationDavosSwitzerland
| | - Tuomas Jartti
- Department of Pediatrics and Adolescent MedicineTurku University Hospital and University of TurkuTurkuFinland
- Department of PediatricsOulu University Hospital and University of OuluOuluFinland
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9
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Nkosi N, Preiser W, van Zyl G, Claassen M, Cronje N, Maritz J, Newman H, McCarthy K, Ntshoe G, Essel V, Korsman S, Hardie D, Smuts H. Molecular characterisation and epidemiology of enterovirus-associated aseptic meningitis in the Western and Eastern Cape Provinces, South Africa 2018-2019. J Clin Virol 2021; 139:104845. [PMID: 33962182 DOI: 10.1016/j.jcv.2021.104845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Enteroviruses are amongst the most common causes of aseptic meningitis. Between November 2018 and May 2019, an outbreak of enterovirus-associated aseptic meningitis cases was noted in the Western and Eastern Cape Provinces, South Africa. OBJECTIVES To describe the epidemiology and phylogeography of enterovirus infections during an aseptic meningitis outbreak in the Western and Eastern Cape Provinces of South Africa. METHODS Cerebrospinal fluid samples from suspected cases were screened using a polymerase chain reaction targeting the 5'UTR. Confirmed enterovirus-associated meningitis samples underwent molecular typing through species-specific VP1/VP2 primers and pan-species VP1 primers. RESULTS Between November 2018 and May 2019, 3497 suspected cases of aseptic meningitis were documented in the Western and Eastern Cape Provinces. Median age was 8 years (range 0-61), interquartile range (IQR=4-13 years), 405/735 (55%) male. 742/3497 (21%) cases were laboratory - confirmed enterovirus positive by routine diagnostic PCR targeting the 5'UTR. 128/742 (17%) underwent molecular typing by VP1 gene sequencing. Echovirus 4 (E4) was detected in 102/128 (80%) cases. Echovirus 9 was found in 7%, Coxsackievirus A13 in 3%. 10 genotypes contributed to the remaining 10% of cases. Synonymous mutations were found in most cases, with sporadic amino acid changes in 13 (12.7%) cases. CONCLUSION The aseptic meningitis outbreak was associated with echovirus 4. Stool samples are valuable for molecular typing in CSF confirmed EV-associated aseptic meningitis.
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Affiliation(s)
- Nokwazi Nkosi
- Division of Medical Virology, Department of Pathology, Stellenbosch University and the National Health Laboratory Service Tygerberg, Cape Town, South Africa.
| | - Wolfgang Preiser
- Division of Medical Virology, Department of Pathology, Stellenbosch University and the National Health Laboratory Service Tygerberg, Cape Town, South Africa
| | - Gert van Zyl
- Division of Medical Virology, Department of Pathology, Stellenbosch University and the National Health Laboratory Service Tygerberg, Cape Town, South Africa
| | - Mathilda Claassen
- Division of Medical Virology, Department of Pathology, Stellenbosch University and the National Health Laboratory Service Tygerberg, Cape Town, South Africa
| | - Nadine Cronje
- Division of Medical Virology, Department of Pathology, Stellenbosch University and the National Health Laboratory Service Tygerberg, Cape Town, South Africa; PathCare Reference Laboratory, N1 City, Goodwood, Cape Town, South Africa
| | - Jean Maritz
- Division of Medical Virology, Department of Pathology, Stellenbosch University and the National Health Laboratory Service Tygerberg, Cape Town, South Africa; PathCare Reference Laboratory, N1 City, Goodwood, Cape Town, South Africa
| | - Howard Newman
- Division of Medical Virology, Department of Pathology, Stellenbosch University and the National Health Laboratory Service Tygerberg, Cape Town, South Africa; PathCare Reference Laboratory, N1 City, Goodwood, Cape Town, South Africa
| | - Kerrigan McCarthy
- Division of Public Health, Surveillance and Response, National Institute of Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Genevie Ntshoe
- Division of Public Health, Surveillance and Response, National Institute of Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa; School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Vivien Essel
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Stephen Korsman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa and the National Health Laboratory Service, Anzio Road, Observatory, Cape Town, South Africa
| | - Diana Hardie
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa and the National Health Laboratory Service, Anzio Road, Observatory, Cape Town, South Africa
| | - Heidi Smuts
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa and the National Health Laboratory Service, Anzio Road, Observatory, Cape Town, South Africa
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10
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Andersson MI, Arancibia-Carcamo CV, Auckland K, Baillie JK, Barnes E, Beneke T, Bibi S, Brooks T, Carroll M, Crook D, Dingle K, Dold C, Downs LO, Dunn L, Eyre DW, Gilbert Jaramillo J, Harvala H, Hoosdally S, Ijaz S, James T, James W, Jeffery K, Justice A, Klenerman P, Knight JC, Knight M, Liu X, Lumley SF, Matthews PC, McNaughton AL, Mentzer AJ, Mongkolsapaya J, Oakley S, Oliveira MS, Peto T, Ploeg RJ, Ratcliff J, Robbins MJ, Roberts DJ, Rudkin J, Russell RA, Screaton G, Semple MG, Skelly D, Simmonds P, Stoesser N, Turtle L, Wareing S, Zambon M. SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus. Wellcome Open Res 2020; 5:181. [PMID: 33283055 PMCID: PMC7689603 DOI: 10.12688/wellcomeopenres.16002.2] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=462 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/494 (0%, 95%CI 0-0.7%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. There was a relationship between RT-PCR negativity and the presence of total SARS-CoV-2 antibody (p=0.02). Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.
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Affiliation(s)
- Monique I. Andersson
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Carcamo
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kathryn Auckland
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - J. Kenneth Baillie
- Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sagida Bibi
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tim Brooks
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Miles Carroll
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Derrick Crook
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kate Dingle
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Louise O. Downs
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Laura Dunn
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - David W. Eyre
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Javier Gilbert Jaramillo
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Heli Harvala
- NHS Blood and Transfusion, 26 Margaret St, Marylebone, London, W1W 8NB, UK
- University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK
| | - Sarah Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Samreen Ijaz
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Tim James
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anita Justice
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Julian C. Knight
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Michael Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Xu Liu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sheila F. Lumley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anna L. McNaughton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Alexander J. Mentzer
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | | | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Marta S. Oliveira
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Rutger J. Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Melanie J. Robbins
- Component Development Laboratory, NHS Blood and Transplant, Cambridge Donor Centre, Cambridge, CB2 0PT, UK
| | - David J. Roberts
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Justine Rudkin
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
- Nuffield Department of Population Health, University Oxford Richard Doll Building, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Rebecca A. Russell
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Gavin Screaton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Peter Simmonds
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Nicole Stoesser
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Susan Wareing
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Maria Zambon
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
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11
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Hayes A, Nguyen D, Andersson M, Antón A, Bailly J, Beard S, Benschop KSM, Berginc N, Blomqvist S, Cunningham E, Davis D, Dembinski JL, Diedrich S, Dudman SG, Dyrdak R, Eltringham GJA, Gonzales‐Goggia S, Gunson R, Howson‐Wells HC, Jääskeläinen AJ, López‐Labrador FX, Maier M, Majumdar M, Midgley S, Mirand A, Morley U, Nordbø SA, Oikarinen S, Osman H, Papa A, Pellegrinelli L, Piralla A, Rabella N, Richter J, Smith M, Söderlund Strand A, Templeton K, Vipond B, Vuorinen T, Williams C, Wollants E, Zakikhany K, Fischer TK, Harvala H, Simmonds P. A European multicentre evaluation of detection and typing methods for human enteroviruses and parechoviruses using RNA transcripts. J Med Virol 2020; 92:1065-1074. [PMID: 31883139 PMCID: PMC7496258 DOI: 10.1002/jmv.25659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/24/2019] [Indexed: 12/28/2022]
Abstract
Polymerase chain reaction (PCR) detection has become the gold standard for diagnosis and typing of enterovirus (EV) and human parechovirus (HPeV) infections. Its effectiveness depends critically on using the appropriate sample types and high assay sensitivity as viral loads in cerebrospinal fluid samples from meningitis and sepsis clinical presentation can be extremely low. This study evaluated the sensitivity and specificity of currently used commercial and in-house diagnostic and typing assays. Accurately quantified RNA transcript controls were distributed to 27 diagnostic and 12 reference laboratories in 17 European countries for blinded testing. Transcripts represented the four human EV species (EV-A71, echovirus 30, coxsackie A virus 21, and EV-D68), HPeV3, and specificity controls. Reported results from 48 in-house and 15 commercial assays showed 98% detection frequencies of high copy (1000 RNA copies/5 µL) transcripts. In-house assays showed significantly greater detection frequencies of the low copy (10 copies/5 µL) EV and HPeV transcripts (81% and 86%, respectively) compared with commercial assays (56%, 50%; P = 7 × 10-5 ). EV-specific PCRs showed low cross-reactivity with human rhinovirus C (3 of 42 tests) and infrequent positivity in the negative control (2 of 63 tests). Most or all high copy EV and HPeV controls were successfully typed (88%, 100%) by reference laboratories, but showed reduced effectiveness for low copy controls (41%, 67%). Stabilized RNA transcripts provide an effective, logistically simple and inexpensive reagent for evaluation of diagnostic assay performance. The study provides reassurance of the performance of the many in-house assay formats used across Europe. However, it identified often substantially reduced sensitivities of commercial assays often used as point-of-care tests.
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Affiliation(s)
- A. Hayes
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - D. Nguyen
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - M. Andersson
- Microbiology Laboratory, John Radcliffe Hospital, Headley Way, HeadingtonOxfordUK
| | - A. Antón
- Respiratory Viruses Unit, Virology Section, Microbiology DepartmentHospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'HebronBarcelonaSpain
| | - J.‐L. Bailly
- Université Clermont Auvergne, LMGE UMR CNRS, UFR MédecineClermont‐FerrandFrance
- CHU Clermont‐Ferrand, National Reference Center for EV and Parechovirus‐Associated LaboratoryClermont‐FerrandFrance
| | - S. Beard
- Enteric Virus Unit, Virus Reference DepartmentNational Infection Service, Public Health EnglandLondonUK
| | - K. S. M. Benschop
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - N. Berginc
- Department for Public Health VirologyNational Laboratory of Health, Environment and FoodLjubljanaSlovenia
| | - S. Blomqvist
- National Institute for Health and Welfare, MannerheimintieHelsinkiFinland
| | - E. Cunningham
- Viapath Infection Sciences, St. Thomas' HospitalLondonUK
| | - D. Davis
- Microbiology, Virology and infection Prevention & ControlGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - J. L. Dembinski
- Department of VirologyNorwegian Institute of Public HealthOsloNorway
| | - S. Diedrich
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch InstituteBerlinGermany
| | - S. G. Dudman
- Department of MicrobiologyOslo University Hospital Rikshospitalet, Inst. Clinical Medicine, University of OsloOsloNorway
| | - R. Dyrdak
- Department of Clinical MicrobiologyKarolinska University HospitalStockholmSweden
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteStockholmSweden
| | - G. J. A. Eltringham
- Molecular Diagnostics Laboratory, Microbiology, Freeman HospitalNewcastle Upon TyneUK
| | - S. Gonzales‐Goggia
- Public Health England Poliovirus Reference Laboratory, National Infection Service, Public Health EnglandLondonUK
| | - R. Gunson
- West of Scotland Specialist Virology CentreGlasgow Royal InfirmaryGlasgowUK
| | - H. C. Howson‐Wells
- Nottingham University Hospitals NHS Trust, Clinical Microbiology, Queens Medical CentreNottinghamUK
| | - A. J. Jääskeläinen
- University of Helsinki and Helsinki University Hospital, HUSLAB, Virology and ImmunologyHelsinkiFinland
| | - F. X. López‐Labrador
- Virology Laboratory, Joint Units in Genomics and Health and Infection and Health, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO‐Public Health)/Universitat de València, Av. CatalunyaValènciaSpain
- CIBEResp, Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, Instituto de Salud Carlos IIIMadridSpain
| | - M. Maier
- Institute of VirologyLeipzig University HospitalLeipzigGermany
| | - M. Majumdar
- The National Institute for Biological Standards and ControlHertfordshireUK
| | - S. Midgley
- Department of Virus and Special Microbiological DiagnosticsVirus Surveillance and Research Section, Statens Serum InstitutCopenhagenDenmark
| | - A. Mirand
- CHU Clermont‐Ferrand, Laboratoire de Virologie—Centre National de Référence des Entérovirus et Parechovirus, Laboratoire Associé—Clermont‐FerrandFrance
| | - U. Morley
- UCD National Virus Reference LaboratoryUniversity College Dublin, BelfieldDublinIreland
| | - S. A. Nordbø
- Department of Medical MicrobiologySt. Olavs University HospitalTrondheimNorway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health SciencesNorwegian University of Science and TechnologyTrondheimNorway
| | - S. Oikarinen
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - H. Osman
- Public Health England Birmingham Public Health Laboratory, Heartlands HospitalBirminghamUK
| | - A. Papa
- Department of MicrobiologyMedical School, Aristotle University of ThessalonikiThessalonikiGreece
| | - L. Pellegrinelli
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
| | - A. Piralla
- Molecular Virology Unit, Microbiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPaviaItaly
| | - N. Rabella
- Virology Section, Santa Creu i Sant Pau University HospitalBarcelonaSpain
| | - J. Richter
- Department of Molecular VirologyCyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - M. Smith
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
- King's College Hospital, Bessemer Wing, Denmark HillLondonUK
| | - A. Söderlund Strand
- Laboratory Medicine, Department of Clinical MicrobiologyLund University Hospital, SölvegatanLundSweden
| | - K. Templeton
- Edinburgh Specialist Virology, Royal Infirmary of EdinburghEdinburghUK
| | - B. Vipond
- Public Health England, South West Regional Laboratory, Pathology Sciences Building, Science QuarterSouthmead HospitalBristolUK
| | - T. Vuorinen
- Clinical MicrobiologyTurku University Hospital and Institute of Biomedicine University of TurkuTurkuFinland
| | | | - E. Wollants
- Clinical and Epidemiological Virology, KU Leuven, REGA Institute, Clinical and Epidemiological VirologyLeuvenBelgium
| | - K. Zakikhany
- Katherina Zakikhany‐Gilg, Public Health Agency of Sweden, Department of MicrobiologyUnit of Laboratory Surveillance of Viral Pathogens and Vaccine Preventable DiseasesStockholmSweden
| | - T. K. Fischer
- CIBEResp, Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, Instituto de Salud Carlos IIIMadridSpain
- Department of Virus and Special Microbiological DiagnosticsVirus Surveillance and Research Section, Statens Serum InstitutCopenhagenDenmark
| | - H. Harvala
- NHS Blood and Transplant, ColindaleLondonUK
| | - P. Simmonds
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
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12
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Andersson MI, Arancibia-Carcamo CV, Auckland K, Baillie JK, Barnes E, Beneke T, Bibi S, Brooks T, Carroll M, Crook D, Dingle K, Dold C, Downs LO, Dunn L, Eyre DW, Gilbert Jaramillo J, Harvala H, Hoosdally S, Ijaz S, James T, James W, Jeffery K, Justice A, Klenerman P, Knight JC, Knight M, Liu X, Lumley SF, Matthews PC, McNaughton AL, Mentzer AJ, Mongkolsapaya J, Oakley S, Oliveira MS, Peto T, Ploeg RJ, Ratcliff J, Robbins MJ, Roberts DJ, Rudkin J, Russell RA, Screaton G, Semple MG, Skelly D, Simmonds P, Stoesser N, Turtle L, Wareing S, Zambon M. SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus. Wellcome Open Res 2020; 5:181. [PMID: 33283055 PMCID: PMC7689603 DOI: 10.12688/wellcomeopenres.16002.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 11/13/2023] Open
Abstract
Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=462 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/494 (0%, 95%CI 0-0.7%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.
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Affiliation(s)
- Monique I. Andersson
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Carcamo
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kathryn Auckland
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - J. Kenneth Baillie
- Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sagida Bibi
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tim Brooks
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Miles Carroll
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Derrick Crook
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kate Dingle
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Louise O. Downs
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Laura Dunn
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - David W. Eyre
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Javier Gilbert Jaramillo
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Heli Harvala
- NHS Blood and Transfusion, 26 Margaret St, Marylebone, London, W1W 8NB, UK
- University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK
| | - Sarah Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Samreen Ijaz
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Tim James
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anita Justice
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Julian C. Knight
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Michael Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Xu Liu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sheila F. Lumley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anna L. McNaughton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Alexander J. Mentzer
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | | | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Marta S. Oliveira
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Rutger J. Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Melanie J. Robbins
- Component Development Laboratory, NHS Blood and Transplant, Cambridge Donor Centre, Cambridge, CB2 0PT, UK
| | - David J. Roberts
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Justine Rudkin
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
- Nuffield Department of Population Health, University Oxford Richard Doll Building, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Rebecca A. Russell
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Gavin Screaton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Peter Simmonds
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Nicole Stoesser
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Susan Wareing
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Maria Zambon
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
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13
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O Loughlin DW, Coughlan S, De Gascun CF, McNally P, Cox DW. The role of rhinovirus infections in young children with cystic fibrosis. J Clin Virol 2020; 129:104478. [PMID: 32521465 PMCID: PMC7263235 DOI: 10.1016/j.jcv.2020.104478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/22/2020] [Accepted: 05/31/2020] [Indexed: 12/29/2022]
Abstract
Rhinovirus (RV) is an important virus in children with chronic respiratory conditions such as asthma; however, little is known about its role in CF. Our aim was to examine the prevalence and clinical impact of different RV species in young children with CF. We collected clinical data and nasal swabs on patients at home and in the hospital setting. Parents filled out symptom diaries and collected nasal swabs when their children were symptomatic and asymptomatic. A novel RV typing PCR assay was used to determine the RV species present. We collected 55 nasal swab samples from ten preschool CF patients over a six month period. The quality of parent collected samples at home was sufficient for PCR analysis. RV was the most common virus detected in young children with CF. There was no difference in the frequency of RV species between symptomatic and asymptomatic subjects. However, parental home-sampling is an acceptable and feasible approach to monitoring young children with CF.
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Affiliation(s)
- D W O Loughlin
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - S Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - C F De Gascun
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - P McNally
- Respiratory Department, Children's Health Ireland, Crumlin, Dublin 12, Ireland; Department of Paediatrics, Royal College of Surgeons in Ireland, Ireland
| | - D W Cox
- Respiratory Department, Children's Health Ireland, Crumlin, Dublin 12, Ireland; School of Medicine, University College Dublin, Dublin 4, Ireland
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14
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Stelzer-Braid S, Wynn M, Chatoor R, Scotch M, Ramachandran V, Teoh HL, Farrar MA, Sampaio H, Andrews PI, Craig ME, MacIntyre CR, Varadhan H, Kesson A, Britton PN, Newcombe J, Rawlinson WD. Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations. J Clin Virol 2019; 122:104216. [PMID: 31790967 DOI: 10.1016/j.jcv.2019.104216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/08/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND The most recent documented Australian outbreak of enterovirus A71 (EV-A71) occurred in Sydney from 2012 to 2013. Over a four-month period more than 100 children presented to four paediatric hospitals with encephalitic presentations including fever and myoclonic jerks. The heterogeneous presentations included typical encephalomyelitis, and cardiopulmonary complications. OBJECTIVES To characterise the genomes of enterovirus strains circulating during the 2013 Sydney EV-A71 outbreak and determine their phylogeny, phylogeography and association between genome and clinical phenotype. STUDY DESIGN We performed an analysis of enterovirus (EV) positive specimens from children presenting to hospitals in the greater Sydney region of Australia during the 2013 outbreak. We amplified near full-length genomes of EV, and used next generation sequencing technology to sequence the virus. We used phylogenetic/phylogeographic analysis to characterize the outbreak viruses. RESULTS We amplified and sequenced 23/63 (37 %) genomes, and identified the majority (61 %) as EV-A71. The EV-A71 sequences showed high level sequence homology to C4a genogroups of EV-A71 circulating in China and Vietnam during 2012-13. Phylogenetic analysis showed EV-A71 strains associated with more severe symptoms, including encephalitis or cardiopulmonary failure, grouped together more closely than those from patients with hand, foot and mouth disease. Amongst the non-EV-A71 sequences were five other EV subtypes (representing enterovirus subtypes A and B), reflecting the diversity of EV co-circulation within the community. CONCLUSIONS This is the first Australian study investigating the near full-length genome of EV strains identified during a known outbreak of EV-A71. EV-A71 sequences were very similar to strains circulating in Asia during the same time period. Whole genome sequencing offers additional information over routine diagnostic testing such as characterisation of emerging recombinant strains and inform vaccine design.
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Affiliation(s)
- Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Matthew Wynn
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Richard Chatoor
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Matthew Scotch
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Public Health and Community Medicine, University of New South Wales, Sydney, NSW 2033, Australia
| | - Vidiya Ramachandran
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Hooi-Ling Teoh
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Michelle A Farrar
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Hugo Sampaio
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Peter Ian Andrews
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Maria E Craig
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - C Raina MacIntyre
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Biosecurity Program, Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia; Watts College of Public Service and Community Solutions, Arizona State University, Phoenix, AZ 85004, USA
| | | | - Alison Kesson
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia; Marie Bashir Institute, University of Sydney, Australia
| | - James Newcombe
- Pathology North, Royal North Shore Hospital, St Leonards, Sydney, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, 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 Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
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15
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Yao LH, Wang C, Wei TL, Wang H, Ma FL, Zheng LS. Human adenovirus among hospitalized children with respiratory tract infections in Beijing, China, 2017-2018. Virol J 2019; 16:78. [PMID: 31196108 PMCID: PMC6567909 DOI: 10.1186/s12985-019-1185-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/24/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Human adenoviruses (HAdVs) cause a wide range of diseases. However, the genotype diversity and epidemiological information relating to HAdVs among hospitalized children with respiratory tract infections (RTIs) is limited. Here, we describe the epidemiology and genotype distribution of HAdVs associated with RTIs in Beijing, China. METHODS Nasopharyngeal aspirates (NPA) were collected from hospitalized children with RTIs from April 2017 to March 2018. HAdVs were detected by a TaqMan-based quantitative real-time polymerase chain reaction (qPCR) assay, and the hexon gene was used for phylogenetic analysis. Epidemiological data were analyzed using statistical product and service solutions (SPSS) 21.0 software. RESULTS HAdV was detected in 72 (5.64%) of the 1276 NPA specimens, with most (86.11%, 62/72) HAdV-positives cases detected among children < 6 years of age. HAdV-B3 (56.06%, 37/66) and HAdV-C2 (19.70%, 13/66) were the most frequent. Of the 72 HAdV-infected cases, 27 (37.50%) were co-infected with other respiratory viruses, most commonly parainfluenza virus (12.50%, 9/72) and rhinovirus (9.72%, 7/72). The log number of viral load ranged from 3.30 to 9.14 copies per mL of NPA, with no significant difference between the HAdV mono- and co-infection groups. The main clinical symptoms in the HAdV-infected patients were fever and cough, and 62 (86.11%, 62/72) were diagnosed with pneumonia. Additionally, HAdVs were detected throughout the year with a higher prevalence in summer. CONCLUSIONS HAdV prevalence is related to age and season. HAdV-B and HAdV-C circulated simultaneously among the hospitalized children with RTIs in Beijing, and HAdV-B type 3 and HAdV-C type 2 were the most frequent.
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Affiliation(s)
- Li-Hong Yao
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Chao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Tian-Li Wei
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Hao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Fen-Lian Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China.
| | - Li-Shu Zheng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China.
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16
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Smuts H, Cronje S, Thomas J, Brink D, Korsman S, Hardie D. Molecular characterization of an outbreak of enterovirus-associated meningitis in Mossel Bay, South Africa, December 2015-January 2016. BMC Infect Dis 2018; 18:709. [PMID: 30594238 PMCID: PMC6311073 DOI: 10.1186/s12879-018-3641-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human enteroviruses (HEVs) are common causal agents of aseptic meningitis in young children. Laboratory and syndromic surveillance during December 2015 and January 2016 noted an unusually high number of paediatric aseptic meningitis cases at a hospital in Mossel Bay, Western Cape Province, South Africa. HEV was detected in clinical samples, prompting an outbreak investigation. METHODS Epidemiological investigations were conducted to ascertain possible linkage between cases. Amplification, sequencing and phylogenetic analysis of the 5'UTR and VP1 regions was undertaken to determine the HEV serotype associated with the outbreak as well as other cases of aseptic meningitis in the area in the preceding 6 weeks. RESULTS Over the 2-month period, 63 CSF samples were available for testing. A total of 43 outbreak cases (68.3%) were observed, and the 26 (60.5%) that could be typed were coxsackie virus A9 (CVA9). Children attending three crèche facilities were epidemiologically linked, accounting for 60.5% (26/43) of the CVA9 cases. The majority of patients were under 10 years of age (55/63, 87.3%) and there was a male predominance (66%). Nucleotide sequence analysis of the 5'UTR and VP1 regions identified 2 lineages of CVA9 co-circulating during the outbreak, although the VP1 capsid protein sequence was identical as all nucleotide differences were synonymous. There was a unique isoleucine at position 64 and all outbreak viruses had a valine to threonine change in the hypervariable BC loop of VP1. Other HEV types circulating in the preceding period were echovirus 30 (n = 4), echovirus 5 (n = 3) and 1 each of echovirus 6, echovirus 9 and echovirus 15. CONCLUSION CVA9 was identified as the pathogen responsible for the large outbreak of aseptic meningitis, with 2 distinct co-circulating lineages.
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Affiliation(s)
- Heidi Smuts
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa and the National Health Laboratory Service, Anzio Road, Observatory, Cape Town, 7925, South Africa.
| | - Sarah Cronje
- Life Bay View Private Hospital, Ryk Tulbach Street & Alhof Drive, De Nova, Mossel Bay, 6506, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases, 1 Modderfontein Road, Sandringham, Johannesburg, 2130, South Africa
| | - Delene Brink
- PathCare George Laboratory, 1 Gloucester Avenue, George, 6529, South Africa
| | - Stephen Korsman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa and the National Health Laboratory Service, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Diana Hardie
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa and the National Health Laboratory Service, Anzio Road, Observatory, Cape Town, 7925, South Africa
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17
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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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18
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Majumdar M, Sharif S, Klapsa D, Wilton T, Alam MM, Fernandez-Garcia MD, Rehman L, Mujtaba G, McAllister G, Harvala H, Templeton K, Mee ET, Asghar H, Ndiaye K, Minor PD, Martin J. Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations. Open Forum Infect Dis 2018; 5:ofy250. [PMID: 30377626 PMCID: PMC6201154 DOI: 10.1093/ofid/ofy250] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/28/2018] [Indexed: 12/17/2022] Open
Abstract
Background Enteroviruses are common human pathogens occasionally associated with severe disease, notoriously paralytic poliomyelitis caused by poliovirus. Other enterovirus serotypes such as enterovirus A71 and D68 have been linked to severe neurological syndromes. New enterovirus serotypes continue to emerge, some believed to be derived from nonhuman primates. However, little is known about the circulation patterns of many enterovirus serotypes and, in particular, the detailed enterovirus composition of sewage samples. Methods We used a next-generation sequencing approach analyzing reverse transcriptase polymerase chain reaction products synthesized directly from sewage concentrates. Results We determined whole-capsid genome sequences of multiple enterovirus strains from all 4 A to D species present in environmental samples from the United Kingdom, Senegal, and Pakistan. Conclusions Our results indicate complex enterovirus circulation patterns in human populations with differences in serotype composition between samples and evidence of sustained and widespread circulation of many enterovirus serotypes. Our analyses revealed known and divergent enterovirus strains, some of public health relevance and genetically linked to clinical isolates. Enteroviruses identified in sewage included vaccine-derived poliovirus and enterovirus D-68 stains, new enterovirus A71 and coxsackievirus A16 genogroups indigenous to Pakistan, and many strains from rarely reported serotypes. We show how this approach can be used for the early detection of emerging pathogens and to improve our understanding of enterovirus circulation in humans.
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Affiliation(s)
- Manasi Majumdar
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom
| | | | - Dimitra Klapsa
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom
| | - Thomas Wilton
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom
| | | | | | | | | | | | | | | | - Edward T Mee
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom
| | - Humayun Asghar
- World Health Organization Eastern Mediterranean Regional Office, Amman, Jordan
| | | | - Philip D Minor
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom
| | - Javier Martin
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom
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19
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McNaughton AL, Sreenu VB, Wilkie G, Gunson R, Templeton K, Leitch ECM. Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype-specific PCR and deep sequencing. J Viral Hepat 2018; 25:524-534. [PMID: 29274184 PMCID: PMC5947153 DOI: 10.1111/jvh.12849] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022]
Abstract
The incidence of mixed genotype hepatitis C virus (HCV) infections in the UK is largely unknown. As the efficacy of direct-acting antivirals is variable across different genotypes, treatment regimens are tailored to the infecting genotype, which may pose issues for the treatment of underlying genotypes within undiagnosed mixed genotype HCV infections. There is therefore a need to accurately diagnose mixed genotype infections prior to treatment. PCR-based diagnostic tools were developed to screen for the occurrence of mixed genotype infections caused by the most common UK genotypes, 1a and 3, in a cohort of 506 individuals diagnosed with either of these genotypes. The overall prevalence rate of mixed infection was 3.8%; however, this rate was unevenly distributed, with 6.7% of individuals diagnosed with genotype 3 harbouring genotype 1a strains and only 0.8% of samples from genotype 1a patients harbouring genotype 3 (P < .05). Mixed infection samples consisted of a major and a minor genotype, with the latter constituting less than 21% of the total viral load and, in 67% of cases, less than 1% of the viral load. Analysis of a subset of the cohort by Illumina PCR next-generation sequencing resulted in a much greater incidence rate than obtained by PCR. This may have occurred due to the nonquantitative nature of the technique and despite the designation of false-positive thresholds based on negative controls.
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Affiliation(s)
- A. L. McNaughton
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK,Present address:
Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - V. B. Sreenu
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - G. Wilkie
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - R. Gunson
- West of Scotland Specialist Virology CentreRoyal Infirmary of GlasgowGlasgowUK
| | | | - E. C. M. Leitch
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
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20
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Harvala H, Jasir A, Penttinen P, Pastore Celentano L, Greco D, Broberg E. Surveillance and laboratory detection for non-polio enteroviruses in the European Union/European Economic Area, 2016. ACTA ACUST UNITED AC 2018; 22. [PMID: 29162204 PMCID: PMC5718392 DOI: 10.2807/1560-7917.es.2017.22.45.16-00807] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Enteroviruses (EVs) cause severe outbreaks of respiratory and neurological disease as illustrated by EV-D68 and EV-A71 outbreaks, respectively. We have mapped European laboratory capacity for identification and characterisation of non-polio EVs to improve preparedness to respond to (re)-emerging EVs linked to severe disease. An online questionnaire on non-polio EV surveillance and laboratory detection was submitted to all 30 European Union (EU)/European Economic Area (EEA) countries. Twenty-nine countries responded; 26 conducted laboratory-based non-polio EV surveillance, and 24 included neurological infections in their surveillance. Eleven countries have established specific surveillance for EV-D68 via sentinel influenza surveillance (n = 7), typing EV-positive respiratory samples (n = 10) and/or acute flaccid paralysis surveillance (n = 5). Of 26 countries performing non-polio EV characterisation/typing, 10 further characterised culture-positive EV isolates, whereas the remainder typed PCR-positive but culture-negative samples. Although 19 countries have introduced sequence-based EV typing, seven still rely entirely on virus isolation. Based on 2015 data, six countries typed over 300 specimens mostly by sequencing, whereas 11 countries characterised under 50 EV-positive samples. EV surveillance activity varied between EU/EEA countries, and did not always specifically target patients with neurological and/or respiratory infections. Introduction of sequence-based typing methods is needed throughout the EU/EEA to enhance laboratory capacity for the detection of EVs.
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Affiliation(s)
- Heli Harvala
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Public Health Agency of Sweden, Stockholm, Sweden
| | - Aftab Jasir
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Pasi Penttinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Donato Greco
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Eeva Broberg
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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21
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Zhou J, Peng Y, Peng X, Gao H, Sun Y, Xie L, Zhong L, Duan Z, Xie Z, Cao Y. Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China. Influenza Other Respir Viruses 2018; 12:279-286. [PMID: 29266860 PMCID: PMC5820417 DOI: 10.1111/irv.12535] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). We aimed to assay the correlation between viral load and clinical characteristics of HBoV and HMPV with LRTI in Changsha, China. METHODS Nasopharyngeal aspirates (NPAs) from children with LRTI were collected. Real-time PCR was used to screen HBoV and HMPV. Analyses were performed using SPSS 16.0 software. RESULTS Pneumonia was the most frequent diagnosis. There was no significant difference between HBoV- and HMPV-positive patients in age (P = .506) or hospitalization duration (P = .280); 24.1% and 18.2% were positive for HBoV and HMPV. HBoV infections peaked in summer (32.2%), and HMPV infections peaked in winter (28.9%). The HBoV-positive patients had a shorter hospitalization duration than the HBoV-negative patients (P = .021), and the HMPV-positive patients had a higher prevalence of fever than the HMPV-negative patients (P = .002). The HBoV viral load was significantly higher among patients aged <1 year (P = .006). The mean HBoV and HMPV viral loads were not significantly different between patients with single infections and coinfections. Patients infected with HBoV only were older than those coinfected with HBoV and other respiratory viruses (P = .005). No significant difference was found in the clinical characteristics of patients infected with HMPV only and those coinfected with HMPV and other respiratory viruses. CONCLUSION Pneumonia was the most frequent diagnosis caused by HBoV and HMPV. Neither HBoV nor HMPV viral load was correlated with disease severity.
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Affiliation(s)
- Jie‐ying Zhou
- Department of Laboratory MedicalThe First People's Hospital of Hunan ChenzhouChenzhouChina
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
- Department of Laboratory MedicalThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Ying Peng
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
- Department of PaediatricsThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Xiao‐you Peng
- Department of Laboratory MedicalThe First People's Hospital of Hunan ChenzhouChenzhouChina
| | - Han‐chun Gao
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
| | - Ya‐ping Sun
- Yuhang District Center for Disease Control and PreventionHangzhouChina
| | - Le‐yun Xie
- Department of PaediatricsThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Li‐li Zhong
- Department of PaediatricsThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Zhao‐jun Duan
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
| | - Zhi‐ping Xie
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
| | - You‐de Cao
- Department of Laboratory MedicalThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
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22
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Borsanyiova M, Kubascikova L, Sarmirova S, Vari SG, Bopegamage S. Assessment of a swab collection method without virus transport medium for PCR diagnosis of coxsackievirus infections. J Virol Methods 2018; 254:18-20. [PMID: 29407208 DOI: 10.1016/j.jviromet.2018.01.010] [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: 07/15/2017] [Revised: 01/18/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022]
Abstract
Classically, detection of human enterovirus (EV) infections is based on virus isolation in tissue culture, proper sample collection and handling that optimizes virus viability. Samples are collected in virus transport medium (VTM) to ensure virus stability. High sensitivity and rapid results have made polymerase chain reaction (PCR) analysis increasingly popular for routine diagnosis. The PCR method enables simple sample collection and storage for EV diagnostics, which may eventually allow self-sampling at home. Our aim was to test a modification of the conventional clinical swab sample collection method for molecular diagnosis of EV infection. We compared swabs (cotton or synthetic) without VTM and the classical standard synthetic swabs with VTM. Effects of storage temperature (+4 °C or -80 °C) and duration were studied. EV-RNA could be detected by reverse transcriptase and nested PCR in both swab types without VTM. Differences depended on the storage duration and temperature. Optimum conditions were immediate processing or storage at -80 °C. Storage without VTM at +4 °C for longer periods is not advisable. We conclude that swabs without VTM can be considered for clinical EV-diagnostics based on PCR, and ultimately for epidemiological sample collection.
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Affiliation(s)
- Maria Borsanyiova
- Enterovirus Laboratory, Faculty of Medicine, Slovak Medical University, Bratislava, Slovak Republic
| | - Lucia Kubascikova
- Enterovirus Laboratory, Faculty of Medicine, Slovak Medical University, Bratislava, Slovak Republic
| | - Sona Sarmirova
- Enterovirus Laboratory, Faculty of Medicine, Slovak Medical University, Bratislava, Slovak Republic
| | - Sandor G Vari
- The International Research and Innovation Management Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shubhada Bopegamage
- Enterovirus Laboratory, Faculty of Medicine, Slovak Medical University, Bratislava, Slovak Republic.
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23
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To KKW, Yip CCY, Yuen KY. Rhinovirus - From bench to bedside. J Formos Med Assoc 2017; 116:496-504. [PMID: 28495415 DOI: 10.1016/j.jfma.2017.04.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 11/16/2022] Open
Abstract
Rhinovirus has been neglected in the past because it was generally perceived as a respiratory virus only capable of causing mild common cold. Contemporary epidemiological studies using molecular assays have shown that rhinovirus is frequently detected in adult and pediatric patients with upper or lower respiratory tract infections. Severe pulmonary and extrapulmonary complications are increasingly recognized. Contrary to popular belief, some rhinoviruses can actually replicate well at 37 °C and infect the lower airway in humans. The increasing availability of multiplex PCR panels allows rapid detection of rhinovirus and provides the opportunity for timely treatment and early recognition of outbreaks. Recent advances in the understanding of host factors for viral attachment and replication, and the host immunological response in both asthmatic and non-asthmatic individuals, have provided important insights into rhinovirus infection which are crucial in the development of antiviral treatment. The identification of novel drugs has been accelerated by repurposing clinically-approved drugs. As humoral antibodies induced by past exposure and vaccine antigen of a particular serotype cannot provide full coverage for all rhinovirus serotypes, novel vaccination strategies are required for inducing protective response against all rhinoviruses.
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Affiliation(s)
- Kelvin K W To
- State Key Laboratory for Emerging Infectious Diseases, Hong Kong Special Administrative Region; Carol Yu Centre for Infection, Hong Kong Special Administrative Region; Research Centre of Infection and Immunology, Hong Kong Special Administrative Region; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Cyril C Y Yip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Hong Kong Special Administrative Region; Carol Yu Centre for Infection, Hong Kong Special Administrative Region; Research Centre of Infection and Immunology, Hong Kong Special Administrative Region; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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24
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Bacterial and viral pathogen spectra of acute respiratory infections in under-5 children in hospital settings in Dhaka city. PLoS One 2017; 12:e0174488. [PMID: 28346512 PMCID: PMC5367831 DOI: 10.1371/journal.pone.0174488] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/09/2017] [Indexed: 02/01/2023] Open
Abstract
The study aimed to examine for the first time the spectra of viral and bacterial pathogens along with the antibiotic susceptibility of the isolated bacteria in under-5 children with acute respiratory infections (ARIs) in hospital settings of Dhaka, Bangladesh. Nasal swabs were collected from 200 under-five children hospitalized with clinical signs of ARIs. Nasal swabs from 30 asymptomatic children were also collected. Screening of viral pathogens targeted ten respiratory viruses using RT-qPCR. Bacterial pathogens were identified by bacteriological culture methods and antimicrobial susceptibility of the isolates was determined following CLSI guidelines. About 82.5% (n = 165) of specimens were positive for pathogens. Of 165 infected cases, 3% (n = 6) had only single bacterial pathogens, whereas 43.5% (n = 87) cases had only single viral pathogens. The remaining 36% (n = 72) cases had coinfections. In symptomatic cases, human rhinovirus was detected as the predominant virus (31.5%), followed by RSV (31%), HMPV (13%), HBoV (11%), HPIV-3 (10.5%), and adenovirus (7%). Streptococcus pneumoniae was the most frequently isolated bacterial pathogen (9%), whereas Klebsiella pneumaniae, Streptococcus spp., Enterobacter agglomerans, and Haemophilus influenzae were 5.5%, 5%, 2%, and 1.5%, respectively. Of 15 multidrug-resistant bacteria, a Klebsiella pneumoniae isolate and an Enterobacter agglomerans isolate exhibited resistance against more than 10 different antibiotics. Both ARI incidence and predominant pathogen detection rates were higher during post-monsoon and winter, peaking in September. Pathogen detection rates and coinfection incidence in less than 1-year group were significantly higher (P = 0.0034 and 0.049, respectively) than in 1–5 years age group. Pathogen detection rate (43%) in asymptomatic cases was significantly lower compared to symptomatic group (P<0.0001). Human rhinovirus, HPIV-3, adenovirus, Streptococcus pneumonia, and Klebsiella pneumaniae had significant involvement in coinfections with P values of 0.0001, 0.009 and 0.0001, 0.0001 and 0.001 respectively. Further investigations are required to better understand the clinical roles of the isolated pathogens and their seasonality.
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25
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Bochkov YA, Watters K, Basnet S, Sijapati S, Hill M, Palmenberg AC, Gern JE. Mutations in VP1 and 3A proteins improve binding and replication of rhinovirus C15 in HeLa-E8 cells. Virology 2016; 499:350-360. [PMID: 27743961 PMCID: PMC5110265 DOI: 10.1016/j.virol.2016.09.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 11/21/2022]
Abstract
Viruses in the rhinovirus C species (RV-C) can cause severe respiratory illnesses in children including pneumonia and asthma exacerbations. A transduced cell line (HeLa-E8) stably expressing the CDHR3-Y529 receptor variant, supports propagation of RV-C after infection. C15 clinical or recombinant isolates replicate in HeLa-E8, however progeny yields are lower than those of related strains of RV-A and RV-B. Serial passaging of C15 in HeLa-E8 resulted in stronger cytopathic effects and increased (≥10-fold) virus binding to cells and progeny yields. The adaptation was acquired by two mutations which increased binding (VP1 T125K) and replication (3A E41K), respectively. A similar 3A mutation engineered into C2 and C41 cDNAs also improved viral replication (2-8 fold) in HeLa but the heparan sulfate mediated cell-binding enhancement by the VP1 change was C15-specific. The findings now enable large-scale cost-effective C15 production by infection and the testing of RV-C infectivity by plaque assay.
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Affiliation(s)
- Yury A Bochkov
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA.
| | - Kelly Watters
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarmila Basnet
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
| | - Shakher Sijapati
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
| | - Marchel Hill
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ann C Palmenberg
- Institute for Molecular Virology, 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
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26
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Superiority of Digital Reverse Transcription-PCR (RT-PCR) over Real-Time RT-PCR for Quantitation of Highly Divergent Human Rhinoviruses. J Clin Microbiol 2016; 55:442-449. [PMID: 27881615 DOI: 10.1128/jcm.01970-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/16/2016] [Indexed: 01/31/2023] Open
Abstract
Human rhinoviruses (HRV) comprise 3 species representing more than 150 genotypes. As an important human respiratory pathogen, molecular detection is an indispensable tool for diagnosis and surveillance. However, the sequence diversity of HRV genotypes poses challenges for developing robust molecular methods that detect all genotypes with equal efficiencies. This study compares the accuracies of reverse transcription-quantitative PCR (RT-qPCR) and reverse transcription-digital PCR (RT-dPCR) for quantifying HRV RNA using genotype-specific primers and probes and a consensus primer/probe set targeting the 5' noncoding region of HRV. When using consensus primers and probes for the quantification of HRV, RT-dPCR outperformed RT-qPCR by consistently and accurately quantifying HRV RNAs across more genotype groups, despite the presence of up to 2 target-sequence mismatches within the primer or probe binding region. Because it does not rely on amplification efficiency, which can be affected by sequence mismatches in primer/probe binding regions, RT-dPCR may be the optimal molecular method for future HRV quantification studies and for quantitating other viruses with high sequence diversity.
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27
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Yan XL, Li YN, Tang YJ, Xie ZP, Gao HC, Yang XM, Li YM, Liu LJ, Duan ZJ. Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection. J Med Virol 2016; 89:589-597. [PMID: 27632796 PMCID: PMC7166468 DOI: 10.1002/jmv.24687] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2016] [Indexed: 11/11/2022]
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are two common viral pathogens in acute lower respiratory tract infections (ALRTI). However, the association of viral load with clinical characteristics is not well‐defined in ALRTI. To explore the correlation between viral load and clinical characteristics of RSV and HMPV in children hospitalized for ALRTI in Lanzhou, China. Three hundred and eighty‐seven children hospitalized for ALRTI were enrolled. Nasopharyngeal aspirates (NPAs) were sampled from each children. Real‐time PCR was used to screen RSV, HMPV, and twelve additional respiratory viruses. Bronchiolitis was the leading diagnoses both in RSV and HMPV positive patients. A significantly greater frequency of wheezing (52% vs. 33.52%, P = 0.000) was noted in RSV positive and negative patients. The RSV viral load was significant higher in children aged <1 year (P = 0.003), children without fever and wheezing (P = 0.015 and P = 0.000), days of illness <14 days (P = 0.002), children with bronchiolitis (P = 0.012) and children with RSV single infections (P = 0.000). No difference was found in the clinical features of HMPV positive and negative patients. The HMPV viral load had no correlation with any clinical characteristics. The incidences of severe disease were similar between single infection and coinfection for the two viruses (RSV, P = 0.221; HMPV, P = 0.764) and there has no statistical significance between severity and viral load (P = 0.166 and P = 0.721). Bronchiolitis is the most common disease caused by RSV and HMPV. High viral load or co‐infection may be associated with some symptoms but neither has a significant impact on disease severity for the two viruses. J. Med. Virol. 89:589–597, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiao-Li Yan
- Department of Pediatrics, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control, Beijing, China
| | - Yu-Ning Li
- Department of Pediatrics, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yi-Jie Tang
- Department of Respiration, Beijing Electric Power Hospital of The North China Grid Company Limited, Beijing, China
| | - Zhi-Ping Xie
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control, Beijing, China
| | - Han-Chun Gao
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control, Beijing, China
| | - Xue-Mei Yang
- Department of Pediatrics, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yu-Mei Li
- Department of Pediatrics, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Li-Jun Liu
- Department of Pediatrics, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Zhao-Jun Duan
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control, Beijing, China
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28
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Reverse transcription genome exponential amplification reaction assay for rapid and universal detection of human rhinoviruses. Arch Virol 2016; 161:1891-8. [PMID: 27132014 DOI: 10.1007/s00705-016-2858-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/04/2016] [Indexed: 10/21/2022]
Abstract
Human rhinoviruses (HRVs) have long been recognized as the cause of more than one-half of acute viral upper respiratory illnesses, and they are associated with more-serious diseases in children, such as asthma, acute otitis media and pneumonia. A rapid and universal test for of HRV infection is in high demand. In this study, a reverse transcription genome exponential amplification reaction (RT-GEAR) assay targeting the HRV 5' untranslated region (UTR) was developed for pan-HRV detection. The reaction was performed in a single tube in one step at 65 °C for 60 min using a real-time fluorometer (Genie(®)II; Optigene). The RT-GEAR assay showed no cross-reactivity with common human enteroviruses, including HEV71, CVA16, CVA6, CVA10, CVA24, CVB5, Echo30, and PV1-3 or with other common respiratory viruses including FluA H3, FluB, PIV1-4, ADV3, RSVA, RSVB and HMPV. With in vitro-transcribed RNA containing the amplified regions of HRV-A60, HRV-B06 and HRV-C07 as templates, the sensitivity of the RT-GEAR assay was 5, 50 and 5 copies/reaction, respectively. Experiments to evaluate the clinical performance of the RT-GEAR assay were also carried out with a panel of 143 previously verified samples, and the results were compared with those obtained using a published semi-nested PCR assay followed by sequencing. The tested panel comprised 91 HRV-negative samples and 52 HRV-positive samples (18 HRV-A-positive samples, 3 HRV-B-positive samples and 31 HRV-C-positive samples). The sensitivity and specificity of the pan-HRVs RT-GEAR assay was 98.08 % and 100 %, respectively. The kappa correlation between the two methods was 0.985. The RT-GEAR assay based on a portable Genie(®)II fluorometer is a sensitive, specific and rapid assay for the universal detection of HRV infection.
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Van Dung N, Anh PH, Van Cuong N, Hoa NT, Carrique-Mas J, Hien VB, Sharp C, Rabaa M, Berto A, Campbell J, Baker S, Farrar J, Woolhouse ME, Bryant JE, Simmonds P. Large-scale screening and characterization of enteroviruses and kobuviruses infecting pigs in Vietnam. J Gen Virol 2015; 97:378-388. [PMID: 26653281 DOI: 10.1099/jgv.0.000366] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A recent survey of pigs in Dong Thap province, Vietnam identified a high frequency of enterovirus species G (EV-G) infection (144/198; 72.7%). Amongst these was a plethora of EV-G types (EV-G1, EV-G6 and four new types EV-G8-EV-G11). To better characterize the genetic diversity of EV-G and investigate the possible existence of further circulating types, we performed a larger-scale study on 484 pig and 45 farm-bred boar faecal samples collected in 2012 and 2014, respectively. All samples from the previous and current studies were also screened for kobuviruses. The overall EV infection frequency remained extremely high (395/484; 81.6%), but with comparable detection rates and viral loads between healthy and diarrhoeic pigs; this contrasted with less frequent detection of EV-G in boars (4/45; 8.9%). EV was most frequently detected in pigs ≤ 14 weeks old (∼ 95%) and declined in older pigs. Infections with EV-G1 and EV-G6 were most frequent, whilst less commonly detected types included EV-G3, EV-G4 and EV-G8-EV-G11, and five new types (EV-G12-EV-G16). In contrast, kobuvirus infection frequency was significantly higher in diarrhoeic pigs (40.9 versus 27.6%; P = 0.01). Kobuviruses also showed contrasting epizootiologies and age associations; a higher prevalence was found in boars (42%) compared with domestic pigs (29%), with the highest infection frequency amongst pigs >52 weeks old. Although genetically diverse, all kobuviruses identified belonged to the species Aichivirus C. In summary, this study confirms infection with EV-G was endemic in Vietnamese domestic pigs and exhibits high genetic diversity and extensive inter-type recombination.
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Affiliation(s)
- Nguyen Van Dung
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Vo Be Hien
- Subdepartment of Animal Health, Dong Thap Province, Vietnam
| | - C Sharp
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - M Rabaa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - A Berto
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - James Campbell
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK.,London School of Hygiene and Tropical Medicine, Keppel Street, Bloomsbury, London WC1E 7HT, UK
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Mark E Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.,Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
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30
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Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis. Virol J 2015; 12:178. [PMID: 26511714 PMCID: PMC4625558 DOI: 10.1186/s12985-015-0408-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detection of specific respiratory viruses is important for surveillance programs, where nasopharyngeal or nasal swabs have traditionally been used. Our objective was to determine whether sampling with a throat swab provides incremental benefit-when used in conjunction with a nasal swab-to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting. FINDINGS Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab. Forty-eight (58 %) patients had virus-positive samples, with 49 virus positives detected by either swab (one patient had a dual viral co-infection). The most common viruses were rhinovirus, coronavirus, and influenza A virus. Specifically, 29 virus positives were detected by both swabs, 14 exclusively by the nasal swab, and six exclusively by the throat swab. The additional six virus positives detected by the throat swab corresponded to an absolute increase in viral detection of 7.1 % (95 % CI: 1.2-12.9 %); the specific viruses detected were four rhinoviruses and two coronaviruses. CONCLUSIONS The flocked nasal swab samples respiratory viruses well, even among patients whose primary complaint is a sore throat. The rayon throat swab has modest incremental value over and above using the flocked nasal mid-turbinate swab alone, which suggests that while throat swabs alone would not be adequate for respiratory viral surveillance, they may have value as a supplementary test.
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Zheng WZ, Wei TL, Ma FL, Yuan WM, Zhang Q, Zhang YX, Cui H, Zheng LS. Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China. Virol J 2015; 12:166. [PMID: 26463646 PMCID: PMC4604616 DOI: 10.1186/s12985-015-0390-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/22/2015] [Indexed: 12/21/2022] Open
Abstract
Background HPyV6 is a novel human polyomavirus (HPyV), and neither its natural history nor its prevalence in human disease is well known. Therefore, the epidemiology and phylogenetic status of HPyV6 must be systematically characterized. Methods The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. The HPyV6-positive specimens were screened for other common respiratory viruses with real-time PCR assays. Results The prevalence of HPyV6 was 1.7 % (15/887), and children ≤ 5 years of age accounted for 80 % (12/15) of cases. All 15 HPyV6-positive patients were coinfected with other respiratory viruses, of which influenza virus A (IFVA) (8/15, 53.3 %) and respiratory syncytial virus (7/15, 46.7 %) were most common. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. The most common symptoms were cough (100 %) and fever (86.7 %). The complete 4926-bp genome (BJ376 strain, GenBank accession number KM387421) was amplified and showed 100 % identity to HPyV6 strain 607a. Conclusions The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Because the coinfection rate was high and the viral load low, it was not possible to establish a correlation between HPyV6 and respiratory diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0390-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen-Zhi Zheng
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China.
| | - Tian-Li Wei
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, 95 Yong An St., Xi-Cheng District, Beijing, 100050, China.
| | - Fen-Lian Ma
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China.
| | - Wu-Mei Yuan
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China.
| | - Qian Zhang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China.
| | - Ya-Xin Zhang
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, 95 Yong An St., Xi-Cheng District, Beijing, 100050, China.
| | - Hong Cui
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, 95 Yong An St., Xi-Cheng District, Beijing, 100050, China.
| | - Li-Shu Zheng
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China.
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Nam YR, Lee U, Choi HS, Lee KJ, Kim N, Jang YJ, Joo CH. Degenerate PCR primer design for the specific identification of rhinovirus C. J Virol Methods 2014; 214:15-24. [PMID: 25483126 PMCID: PMC7113658 DOI: 10.1016/j.jviromet.2014.10.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 10/15/2014] [Accepted: 10/21/2014] [Indexed: 12/04/2022]
Abstract
Degenerate primer design based on multiple sequence alignments. HEV primer set for the identification of all enteroviruses by RT-PCR. HRVC primer set for the specific identification of rhinovirus C by RT-PCR.
Human rhinovirus (HRV)-A and -B is a common cause of upper respiratory tract infections. Recently, a third species, HRV-C, was categorized based on molecular typing studies. The results showed that the HRV-C genome had diverged from that of HRV-A and -B. Despite its late identification, increasing evidence suggests that HRV-C causes more severe pathogenic infections than HRV-A or -B; however, a large amount of epidemiological data is required to confirm this association in different clinical settings. Consequently, a simple and rapid method for identifying HRV-C is required to expedite such epidemiological studies. Here, two degenerate primer sets (HEV and HRVC) were designed based on bioinformatic analyses. The HEV set targeting the fifth IRES domain sequence within the 5′-UTR, which is highly conserved among enteroviruses, was designed to detect all enteroviruses, whereas the HRVC set, which targeted the VP2 coding region, was designed to detect HRV-C alone. Both primer sets were tested against a panel of standard enteroviruses and clinical lavage samples. HEV detected all enteroviruses tested whereas HRVC was specific for HRV-C. Although the primer design strategy was confirmed with a limited number of samples, extensive tests are required to be applied in clinical settings.
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Affiliation(s)
- Young Ran Nam
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Uk Lee
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Han Seok Choi
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kyoung Jin Lee
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Nari Kim
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong Ju Jang
- Department of Otolaryngology, Asan Medical Center, Seoul, Republic of Korea
| | - Chul Hyun Joo
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea; Cell Dysfunction Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Abstract
BACKGROUND The symptoms observed in children with human parechovirus (HPeV) infection vary widely from asymptomatic or mild gastrointestinal infections to more severe central nervous system infections and sepsis-like disease. Many of the disease associations are, however, only suggestive. In this study, we examined the connection between HPeV and acute otitis media, lower respiratory infections and suspected central nervous system infections. METHODS An HPeV specific real-time reverese transcriptase polymerase chain reaction was used to detect HPeV RNA. We analyzed altogether 200 middle-ear fluid samples, 192 nasopharyngeal aspirates, 79 cerebrospinal fluid specimens and 50 serum and 5 fecal or fecal culture samples. Positive samples were typed by sequencing the VP1 region. RESULTS Seven (8%) of 85 children with suspected central nervous system infections were positive for HPeV. Of these, 4 (all in autumn 2012 and from children <3 months of age) were typed to be HPeV4, whereas 1 child had HPeV3. HPeV4 was detected from stool, serum and cerebrospinal fluid. The children with acute otitis media tested HPeV positive in 2.5% episodes. In the lower respiratory cases, HPeV was absent. CONCLUSIONS The findings reported in this study suggest that HPeV4 can cause sepsis-like disease in young infants and be present in cerebrospinal fluid. Furthermore, this report shows that HPeV findings in children with more severe symptoms occur also in Finland.
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Shaukat S, Angez M, Alam MM, Jebbink MF, Deijs M, Canuti M, Sharif S, de Vries M, Khurshid A, Mahmood T, van der Hoek L, Zaidi SSZ. Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA. Virol J 2014; 11:146. [PMID: 25112200 PMCID: PMC4254409 DOI: 10.1186/1743-422x-11-146] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Methods VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers. Results Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community. Conclusion Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-146) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan.
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Harvala H, Griffiths M, Solomon T, Simmonds P. Distinct systemic and central nervous system disease patterns in enterovirus and parechovirus infected children. J Infect 2014; 69:69-74. [DOI: 10.1016/j.jinf.2014.02.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 02/11/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
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Harvala H, Calvert J, Van Nguyen D, Clasper L, Gadsby N, Molyneaux P, Templeton K, McWilliams Leitch C, Simmonds P. Comparison of diagnostic clinical samples and environmental sampling for enterovirus and parechovirus surveillance in Scotland, 2010 to 2012. ACTA ACUST UNITED AC 2014; 19. [PMID: 24762664 DOI: 10.2807/1560-7917.es2014.19.15.20772] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Human enteroviruses (EV) and parechoviruses (HPeV) within the family Picornaviridae are the most common causes of viral central nervous system (CNS)-associated infections including meningitis and neonatal sepsis-like disease. The frequencies of EV and HPeV types identified in clinical specimens collected in Scotland over an eight-year period were compared to those identified in sewage surveillance established in Edinburgh. Of the 35 different EV types belonging to four EV species (A to D) and the four HPeV types detected in this study, HPeV3 was identified as the most prevalent picornavirus in cerebrospinal fluid samples, followed by species B EV. Interestingly, over half of EV and all HPeV CNS-associated infections were observed in young infants (younger than three months). Detection of species A EV including coxsackievirus A6 and EV71 in clinical samples and sewage indicates that these viruses are already widely circulating in Scotland. Furthermore, species C EV were frequently identified EV in sewage screening but they were not present in any of 606 EV-positive clinical samples studied, indicating their likely lower pathogenicity. Picornavirus surveillance is important not only for monitoring the changing epidemiology of these infections but also for the rapid identification of spread of emerging EV and/or HPeV types.
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Affiliation(s)
- H Harvala
- Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh United Kingdom
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High rates of infection with novel enterovirus variants in wild populations of mandrills and other old world monkey species. J Virol 2014; 88:5967-76. [PMID: 24623420 DOI: 10.1128/jvi.00088-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED Enteroviruses (EVs) are a genetically and antigenically diverse group of viruses infecting humans. A mostly distinct set of EV variants have additionally been documented to infect wild apes and several, primarily captive, Old World monkey (OWM) species. To investigate the prevalence and genetic characteristics of EVs infecting OWMs in the wild, fecal samples from mandrills (Mandrillus sphinx) and other species collected in remote regions of southern Cameroon were screened for EV RNA. Remarkably high rates of EV positivity were detected in M. sphinx (100 of 102 screened), Cercocebus torquatus (7/7), and Cercopithecus cephus (2/4), with high viral loads indicative of active infection. Genetic characterization in VP4/VP2 and VP1 regions allowed EV variants to be assigned to simian species H (EV-H) and EV-J (including one or more new types), while seven matched simian EV-B variants, SA5 and EV110 (chimpanzee). Sequences from the remaining 70 formed a new genetic group distinct in VP4/2 and VP1 region from all currently recognized human or simian EV species. Complete genome sequences were obtained from three to determine their species assignment. In common with EV-J and the EV-A A13 isolate, new group sequences were chimeric, being most closely related to EV-A in capsid genes and to EV-B in the nonstructural gene region. Further recombination events created different groupings in 5' and 3' untranslated regions. While clearly a distinct EV group, the hybrid nature of new variants prevented their unambiguous classification as either members of a new species or as divergent members of EV-A using current International Committee on Taxonomy of Viruses (ICTV) assignment criteria. IMPORTANCE This study is the first large-scale investigation of the frequency of infection and diversity of enteroviruses (EVs) infecting monkeys (primarily mandrills) in the wild. Our findings demonstrate extremely high frequencies of active infection (95%) among mandrills and other Old World monkey species inhabiting remote regions of Cameroon without human contact. EV variants detected were distinct from those infecting human populations, comprising members of enterovirus species B, J, and H and a large novel group of viruses most closely related to species A in the P1 region. The viral sequences obtained contribute substantially to our growing understanding of the genetic diversity of EVs and the existence of interspecies chimerism that characterizes the novel variants in the current study, as well as in previously characterized species A and J viruses infecting monkeys. The latter findings will contribute to future development of consensus criteria for species assignments in enteroviruses and other picornavirus genera.
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Chen J, Fu Y, Ju L, Miao X, Shen Y, He L, Wang W, Jin J, Shao L, Sampath R, Ecker DJ, Zhang Y, Li M, Cheng X, Zhang W. Detection and identification of viral pathogens in patients with hand, foot, and mouth disease by multilocus PCR, reverse-transcription PCR and electrospray ionization mass spectrometry. J Clin Virol 2014; 59:115-9. [DOI: 10.1016/j.jcv.2013.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 11/25/2022]
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McWilliam Leitch EC, McLauchlan J. Determining the cellular diversity of hepatitis C virus quasispecies by single-cell viral sequencing. J Virol 2013; 87:12648-55. [PMID: 24049174 PMCID: PMC3838117 DOI: 10.1128/jvi.01602-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/07/2013] [Indexed: 12/15/2022] Open
Abstract
Single-cell genomics is emerging as an important tool in cellular biology. We describe for the first time a system to investigate RNA virus quasispecies diversity at the cellular level utilizing hepatitis C virus (HCV) replicons. A high-fidelity nested reverse transcription (RT)-PCR assay was developed, and validation using control transcripts of known copy number indicated a detection limit of 3 copies of viral RNA/reaction. This system was used to determine the cellular diversity of subgenomic JFH-1 HCV replicons constitutively expressed in Huh7 cells. Each cell contained a unique quasispecies that was much less diverse than the quasispecies of the bulk cell population from which the single cells were derived, suggesting the occurrence of independent evolution at the cellular level. An assessment of the replicative fitness of the predominant single-cell quasispecies variants indicated a modest reduction in fitness compared to the wild type. Real-time RT-PCR methods capable of determining single-cell viral loads were developed and indicated an average of 113 copies of replicon RNA per cell, correlating with calculated RNA copy numbers in the bulk cell population. This study introduces a single-cell RNA viral-sequencing method with numerous potential applications to explore host-virus interactions during infection. HCV quasispecies diversity varied greatly between cells in vitro, suggesting different within-cell evolutionary pathways. Such divergent trajectories in vivo could have implications for the evolution and establishment of antiviral-resistant variants and host immune escape mutants.
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Luoto R, Ruuskanen O, Waris M, Kalliomäki M, Salminen S, Isolauri E. Prebiotic and probiotic supplementation prevents rhinovirus infections in preterm infants: a randomized, placebo-controlled trial. J Allergy Clin Immunol 2013; 133:405-13. [PMID: 24131826 PMCID: PMC7112326 DOI: 10.1016/j.jaci.2013.08.020] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 08/15/2013] [Accepted: 08/26/2013] [Indexed: 12/28/2022]
Abstract
Background Simple and safe strategies for the prevention of viral respiratory tract infections (RTIs) are needed. Objective We hypothesized that early prebiotic or probiotic supplementation would reduce the risk of virus-associated RTIs during the first year of life in a cohort of preterm infants. Methods In this randomized, double-blind, placebo-controlled trial (ClinicalTrials.gov no. NCT00167700), 94 preterm infants (gestational age, ≥32 + 0 and ≤36 + 6 weeks; birth weight, >1500 g) treated at Turku University Hospital, Turku, Finland, were allocated to receive oral prebiotics (galacto-oligosaccharide and polydextrose mixture, 1:1), a probiotic (Lactobacillus rhamnosus GG, ATCC 53103), or placebo (microcrystalline cellulose) between days 3 and 60 of life. The primary outcome was the incidence of clinically defined virus-associated RTI episodes confirmed from nasal swabs by using nucleic acid testing. Secondary outcomes were the severity and duration of RTIs. Results A significantly lower incidence of RTIs was detected in infants receiving prebiotics (rate ratio [RR], 0.24; 95% CI, 0.12-0.49; P < .001) or probiotics (RR, 0.50; 95% CI, 0.28-0.90; P = .022) compared with those receiving placebo. Also, the incidence of rhinovirus-induced episodes, which comprised 80% of all RTI episodes, was found to be significantly lower in the prebiotic (RR, 0.31; 95% CI, 0.14-0.66; P = .003) and probiotic (RR, 0.49; 95% CI, 0.24-1.00; P = .051) groups compared with the placebo group. No differences emerged among the study groups in rhinovirus RNA load during infections, duration of rhinovirus RNA shedding, duration or severity of rhinovirus infections, or occurrence of rhinovirus RNA in asymptomatic infants. Conclusions Gut microbiota modification with specific prebiotics and probiotics might offer a novel and cost-effective means to reduce the risk of rhinovirus infections.
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Affiliation(s)
- Raakel Luoto
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland.
| | - Olli Ruuskanen
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Matti Waris
- Department of Virology, University of Turku, Turku, Finland
| | - Marko Kalliomäki
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Erika Isolauri
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
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Simultaneous detection and differentiation of human rhino- and enteroviruses in clinical specimens by real-time PCR with locked nucleic Acid probes. J Clin Microbiol 2013; 51:3960-7. [PMID: 24048533 DOI: 10.1128/jcm.01646-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Human rhinoviruses (HRVs) and human enteroviruses (HEVs) are significant respiratory pathogens. While HRV infections are restricted to the respiratory tract, HEV infections may spread to secondary target organs. The method of choice for sensitive specific detection of these viruses is reverse transcription (RT)-PCR with primers targeting the conserved 5' noncoding region of the viral RNA. On the other hand, sequence similarities between HRVs and HEVs complicate their differential detection. In this study, we describe the use of locked nucleic acid (LNA) analogues in short double-dye probes which contained only two selectively HRV- or HEV-specific bases. The double-stranded DNA dye BOXTO (4-[6-(benzoxazole-2-yl-(3-methyl-)-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)]-1-methyl-quinolinium chloride) was used with the LNA probes in a tricolor real-time PCR assay to allow specific detection of HRVs (probes labeled with 6-carboxyfluorescein [FAM] [green]) and HEVs (Cy5 [red]) with additional melting curve analysis (BOXTO [yellow]). The functionality of the probes was validated in PCR and RT-PCR assays using plasmids containing viral cDNA, quantified viral RNA transcripts, cultivated rhino- and enterovirus prototypes, and clinical specimens. Of 100 HRV and 63 HEV prototypes, the probes correctly identified all HEVs except one that produced only a BOXTO signal. Among 118 clinical specimens with sequencing results, concordant results were obtained for 116 specimens. Two specimens were reactive with both probes, but sequencing yielded only a single virus. Real-time PCR with LNA probes allowed sensitive group-specific identification of HRVs and HEVs and would enable relative copy number determination. The assay is suitable for rapid and accurate differential detection of HRVs and HEVs in a diagnostic laboratory setting.
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Peltola V, Waris M, Kainulainen L, Kero J, Ruuskanen O. Virus shedding after human rhinovirus infection in children, adults and patients with hypogammaglobulinaemia. Clin Microbiol Infect 2013; 19:E322-7. [PMID: 23490188 DOI: 10.1111/1469-0691.12193] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/10/2013] [Accepted: 02/11/2013] [Indexed: 11/29/2022]
Abstract
The shedding of human rhinovirus (HRV) after an acute, naturally acquired infection has not been described in detail. We determined the duration of HRV shedding in immunocompetent children and adults, and in patients with primary hypogammaglobulinaemia. Subjects with symptoms of respiratory tract infection, and their household contacts, were screened for HRV by reverse transcription PCR. They were followed by serial, self-collected nasal swab specimens until negative for HRV or infected by another HRV type. We followed 62 HRV infections in 54 subjects. The mean (95% CI) duration of HRV shedding was 11.4 (8.2-14.7) days in children, 10.1 (7.4-12.9) days in adults, and 40.9 (26.4-55.4) days in patients with hypogammaglobulinaemia (p <0.001). The duration of respiratory tract symptoms correlated with the duration of virus shedding (p 0.002). A new infection by another HRV type soon after the first episode was common. We conclude that the shedding times of HRV are relatively short in otherwise healthy individuals. In contrast, prolonged shedding over 28 days is frequent in patients with hypogammaglobulinaemia despite immunoglobulin replacement therapy.
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Affiliation(s)
- V Peltola
- Department of Paediatrics, Turku University Hospital, Turku, Finland.
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