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Hou M, Liu G, Meng C, Dong L, Fang Y, Wang L, Wang N, Cai C, Wang H. Circulation patterns and molecular characteristics of respiratory syncytial virus among hospitalized children in Tianjin, China, before and during the COVID-19 pandemic (2017-2022). Virol Sin 2024:S1995-820X(24)00114-7. [PMID: 39067791 DOI: 10.1016/j.virs.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/24/2024] [Indexed: 07/30/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the main pathogen that causes hospitalization for acute lower respiratory tract infections (ALRIs) in children. With the reopening of communities and schools, the resurgence of RSV in the COVID-19 post-pandemic era has become a major concern. To understand the circulation patterns and genotype variability of RSV in Tianjin before and during the COVID-19 pandemic, a total of 19,531 nasopharyngeal aspirate samples from hospitalized children in Tianjin from July 2017 to June 2022 were evaluated. Direct immunofluorescence and polymerase chain reaction (PCR) were used for screening RSV-positive samples and subtyping, respectively. Further analysis of mutations in the second hypervariable region (HVR2) of the G gene was performed through Sanger sequencing. Our results showed that 16.46% (3,215/19,531) samples were RSV positive and a delayed increase in the RSV infection rates occurred in the winter season from December 2020 to February 2021, with the average RSV-positive rate of 35.77% (519/1,451). The ON1, with H258Q and H266L substitutions, and the BA9, with T290I and T312I substitutions, are dominant strains that alternately circulate every 1-2 years in Tianjin, China, from July 2017 to June 2022. In addition, novel substitutions, such as N296Y, K221T, N230K, V251A in the BA9 genotype, and L226I in the ON1 genotype, emerged during the COVID-19 pandemic. Analysis of clinical characteristics indicated no significant differences between RSV-A and RSV-B groups. This study provides a theoretical basis for clinical prevention and treatment. However, further studies are needed to explore the regulatory mechanism of host immune responses to different lineages of ON1 and BA9 in the future.
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Affiliation(s)
- Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Guangping Liu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Chao Meng
- Department of Medical Laboratory, Tianjin Second People's Hospital, Tianjin, 300192, China
| | - Lili Dong
- Department of Respiratory, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, 300134, China
| | - Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Ning Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Hanjie Wang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China.
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Madi N, Safar HA, Al-Adwani A, Sadeq M, Al-Turab M. Genomic characterization of circulating human respiratory syncytial viruses A and B in Kuwait using whole-genome sequencing. Microbiol Spectr 2024; 12:e0015924. [PMID: 38808977 PMCID: PMC11218466 DOI: 10.1128/spectrum.00159-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
The human respiratory syncytial virus (RSV) is considered one of the most common viruses that infect children globally. The virus is known to have extensive gene sequence variability within and between RSV groups A and B globally; however, there is no information on the whole-genome characterization and diversity of RSV in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with acute respiratory tract infection (ARTI) in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with ARTI in Kuwait. Between January 2020 and September 2022, 7,093 respiratory samples were collected from hospitalized infants, children, and adults and were analyzed for respiratory viruses by multiplex real-time PCR. Whole-genome sequencing using the Oxford Nanopore sequencing technology was performed on 84 RSV-positive samples. The results revealed a higher prevalence of group A (76%) than group B (24%) RSV isolates. Phylogenetic analysis showed that RSV-A strains clustered with the GA2.3.5 sub-genotype and RSV-B strains clustered with the GB5.0.5a sub-genotype; however, forming new lineages of RSV-A and RSV-B circulated in Kuwait during this period. Genetic variability was higher among the group A viruses than group B viruses, and the rate of synonymous and missense mutations was high in genes other than the G protein-coding gene. We also detected several known and unique molecular markers in different protein-coding genes. This is the first study in Kuwait to characterize the whole genomes of RSV A and B to identify the circulating genotypes, comprehend the genetic diversity and the evolution of the virus, and identify important genetic markers associated with specific genotypes.IMPORTANCEWhole-genome sequencing of respiratory syncytial virus (RSV) strains in Kuwait using MinION Nanopore technology was used to characterize and analyze the genotypes and sub-genotypes of the RSV circulating among patients with acute respiratory tract infections in Kuwait. This study also identified known and unknown gene mutations and imported genetic markers associated with specific genotypes. These results will assist in establishing a framework for RSV classification and allow for a better consideration of the mechanisms leading to the generation of diversity of RSV. In addition, these data will allow a comparison of vaccine viruses with those in Kuwait, providing useful insights into future vaccine and therapy strategies for RSV in Kuwait.
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Affiliation(s)
- Nada Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Hussain A. Safar
- Research Core Facility and OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Anfal Al-Adwani
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Mohammed Sadeq
- Jaber Al-Ahmad Armed Forces Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Mariam Al-Turab
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
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Alchikh M, Conrad TOF, Obermeier PE, Ma X, Schweiger B, Opota O, Rath BA. Disease Burden and Inpatient Management of Children with Acute Respiratory Viral Infections during the Pre-COVID Era in Germany: A Cost-of-Illness Study. Viruses 2024; 16:507. [PMID: 38675850 PMCID: PMC11054359 DOI: 10.3390/v16040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Respiratory viral infections (RVIs) are common reasons for healthcare consultations. The inpatient management of RVIs consumes significant resources. From 2009 to 2014, we assessed the costs of RVI management in 4776 hospitalized children aged 0-18 years participating in a quality improvement program, where all ILI patients underwent virologic testing at the National Reference Centre followed by detailed recording of their clinical course. The direct (medical or non-medical) and indirect costs of inpatient management outside the ICU ('non-ICU') versus management requiring ICU care ('ICU') added up to EUR 2767.14 (non-ICU) vs. EUR 29,941.71 (ICU) for influenza, EUR 2713.14 (non-ICU) vs. EUR 16,951.06 (ICU) for RSV infections, and EUR 2767.33 (non-ICU) vs. EUR 14,394.02 (ICU) for human rhinovirus (hRV) infections, respectively. Non-ICU inpatient costs were similar for all eight RVIs studied: influenza, RSV, hRV, adenovirus (hAdV), metapneumovirus (hMPV), parainfluenza virus (hPIV), bocavirus (hBoV), and seasonal coronavirus (hCoV) infections. ICU costs for influenza, however, exceeded all other RVIs. At the time of the study, influenza was the only RVI with antiviral treatment options available for children, but only 9.8% of influenza patients (non-ICU) and 1.5% of ICU patients with influenza received antivirals; only 2.9% were vaccinated. Future studies should investigate the economic impact of treatment and prevention of influenza, COVID-19, and RSV post vaccine introduction.
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Affiliation(s)
- Maren Alchikh
- Vaccine Safety Initiative, 10437 Berlin, Germany; (M.A.); (P.E.O.)
- Laboratoire Chrono-Environnement, Université Bourgogne Franche-Comté, 25030 Besançon, France
- ESGREV (ESCMID Respiratory Virus Study Group), 4001 Basel, Switzerland;
| | | | - Patrick E. Obermeier
- Vaccine Safety Initiative, 10437 Berlin, Germany; (M.A.); (P.E.O.)
- ESGREV (ESCMID Respiratory Virus Study Group), 4001 Basel, Switzerland;
| | - Xiaolin Ma
- Department of Pulmonology, Capital Institute of Pediatrics, Beijing 100005, China;
| | - Brunhilde Schweiger
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Reference Centre for Influenza, Robert Koch-Institute, 13353 Berlin, Germany;
| | - Onya Opota
- ESGREV (ESCMID Respiratory Virus Study Group), 4001 Basel, Switzerland;
- Institute of Microbiology, University of Lausanne, 1011 Lausanne, Switzerland
| | - Barbara A. Rath
- Vaccine Safety Initiative, 10437 Berlin, Germany; (M.A.); (P.E.O.)
- Laboratoire Chrono-Environnement, Université Bourgogne Franche-Comté, 25030 Besançon, France
- ESGREV (ESCMID Respiratory Virus Study Group), 4001 Basel, Switzerland;
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Deng S, Guo L, Cohen C, Meijer A, Moyes J, Pasittungkul S, Poovorawan Y, Teirlinck A, van Boven M, Wanlapakorn N, Wolter N, Paget J, Nair H, Li Y. Impact of Subgroup Distribution on Seasonality of Human Respiratory Syncytial Virus: A Global Systematic Analysis. J Infect Dis 2024; 229:S25-S33. [PMID: 37249267 DOI: 10.1093/infdis/jiad192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/18/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Previous studies reported inconsistent findings regarding the association between respiratory syncytial virus (RSV) subgroup distribution and timing of RSV season. We aimed to further understand the association by conducting a global-level systematic analysis. METHODS We compiled published data on RSV seasonality through a systematic literature review, and unpublished data shared by international collaborators. Using annual cumulative proportion (ACP) of RSV-positive cases, we defined RSV season onset and offset as ACP reaching 10% and 90%, respectively. Linear regression models accounting for meteorological factors were constructed to analyze the association of proportion of RSV-A with the corresponding RSV season onset and offset. RESULTS We included 36 study sites from 20 countries, providing data for 179 study-years in 1995-2019. Globally, RSV subgroup distribution was not significantly associated with RSV season onset or offset globally, except for RSV season offset in the tropics in 1 model, possibly by chance. Models that included RSV subgroup distribution and meteorological factors explained only 2%-4% of the variations in timing of RSV season. CONCLUSIONS Year-on-year variations in RSV season onset and offset are not well explained by RSV subgroup distribution or meteorological factors. Factors including population susceptibility, mobility, and viral interference should be examined in future studies.
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Affiliation(s)
- Shuyu Deng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ling Guo
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adam Meijer
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Siripat Pasittungkul
- Centre of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Centre of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Anne Teirlinck
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Michiel van Boven
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Nasamon Wanlapakorn
- Centre of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - John Paget
- Netherlands Institute for Health Services Research, Utrecht, The Netherlands
| | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - You Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
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Valley‐Omar Z, Tempia S, Hellferscee O, Walaza S, Variava E, Dawood H, Kahn K, McMorrow M, Pretorius M, Mtshali S, Mamorobela E, Wolter N, Venter M, von Gottberg A, Cohen C, Treurnicht FK. Human respiratory syncytial virus diversity and epidemiology among patients hospitalized with severe respiratory illness in South Africa, 2012-2015. Influenza Other Respir Viruses 2022; 16:222-235. [PMID: 34528769 PMCID: PMC8818822 DOI: 10.1111/irv.12905] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND We aimed to describe the prevalence of human respiratory syncytial virus (HRSV) and evaluate associations between HRSV subgroups and/or genotypes and epidemiologic characteristics and clinical outcomes in patients hospitalized with severe respiratory illness (SRI). METHODS Between January 2012 and December 2015, we enrolled patients of all ages admitted to two South African hospitals with SRI in prospective hospital-based syndromic surveillance. We collected respiratory specimens and clinical and epidemiological data. Unconditional random effect multivariable logistic regression was used to assess factors associated with HRSV infection. RESULTS HRSV was detected in 11.2% (772/6908) of enrolled patients of which 47.0% (363/772) were under the age of 6 months. There were no differences in clinical outcomes of HRSV subgroup A-infected patients compared with HRSV subgroup B-infected patients but among patients aged <5 years, children with HRSV subgroup A were more likely be coinfected with Streptococcus pneumoniae (23/208, 11.0% vs. 2/90, 2.0%; adjusted odds ratio 5.7). No significant associations of HRSV A genotypes NA1 and ON1 with specific clinical outcomes were observed. CONCLUSIONS While HRSV subgroup and genotype dominance shifted between seasons, we showed similar genotype diversity as noted worldwide. We found no association between clinical outcomes and HRSV subgroups or genotypes.
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Affiliation(s)
- Ziyaad Valley‐Omar
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of Cape TownCape TownSouth Africa
| | - Stefano Tempia
- Centers for Disease Control and PreventionPretoriaSouth Africa
- Centers for Disease Control and PreventionAtlantaGeorgiaUSA
- MassGenicsDuluthGeorgiaUSA
- University of the WitwatersrandJohannesburgSouth Africa
| | - Orienka Hellferscee
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| | - Sibongile Walaza
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | | | - Halima Dawood
- University of KwaZulu‐NatalKwaZulu‐NatalSouth Africa
- Greys hospitalPietermaritzburgSouth Africa
| | - Kathleen Kahn
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| | - Meredith McMorrow
- Centers for Disease Control and PreventionPretoriaSouth Africa
- Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Marthi Pretorius
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- Novartis Pharma AGBaselSwitzerland
| | - Senzo Mtshali
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| | - Ernest Mamorobela
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Marietjie Venter
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of PretoriaPretoriaSouth Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Florette K. Treurnicht
- University of the WitwatersrandJohannesburgSouth Africa
- National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic HospitalJohannesburgSouth Africa
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Tabatabai J, Ihling CM, Rehbein RM, Schnee SV, Hoos J, Pfeil J, Grulich-Henn J, Schnitzler P. Molecular epidemiology of respiratory syncytial virus in hospitalised children in Heidelberg, Southern Germany, 2014-2017. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105209. [PMID: 35032683 DOI: 10.1016/j.meegid.2022.105209] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the leading cause of hopitalisation in young children with respiratory tract infections (RTI). The aim of this research project was to analyse RSV genotypes and the diversification of RSV strains among hospitalised children in Heidelberg, Germany. METHODS We prospectively analysed nasopharyngeal swabs (NPS) from children who were hospitalised with acute RTI at the University Hospital Heidelberg, Germany, during winter seasons 2014 to 2017. RSV RT-PCR and RSV sequence analysis of the G gene coding for the attachment glycoprotein were performed. Clinical data was obtained using a standardised questionnaire. RESULTS RSV was detected in 405 out of 946 samples from hospitalised children. Most RSV positive children were below the age of two years (84.4%) and had a lower RTI (78.8%). The majority of RSV positive children was male, significantly younger than RSV negative children with a median age of 0.39 years and with more severe respiratory symptoms. Out of 405 positive samples, 317 RSV strains were successfully sub-grouped into RSV subtypes A (57.4%; 182/317) and B (42.6%; 135/317). Both RSV subtypes cocirculated in all analysed winter seasons. Phylogenetic analysis of 317 isolates revealed that the majority of RSV-A strains (180/182) belonged to the ON1 genotype, most RSV-B strains could be attributed to the BAIX genotype (132/135). ON1 and BAIX strains showed a sub-differentiation into different lineages and we were able to identify new (sub)genotypes. CONCLUSION Analysis of the molecular epidemiology of RSV from different seasons revealed the cocirculation and diversification of RSV genotypes ON1 and BAIX.
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Affiliation(s)
- J Tabatabai
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; German Centre for Infectious Diseases (DZIF), Heidelberg, Germany; Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany.
| | - C M Ihling
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; German Centre for Infectious Diseases (DZIF), Heidelberg, Germany; Dr. von Haunersches Kinderspital, University Hospital of the LMU Munich, Munich, Germany
| | - R M Rehbein
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; German Centre for Infectious Diseases (DZIF), Heidelberg, Germany; Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - S V Schnee
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; German Centre for Infectious Diseases (DZIF), Heidelberg, Germany
| | - J Hoos
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; German Centre for Infectious Diseases (DZIF), Heidelberg, Germany; Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - J Pfeil
- Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - J Grulich-Henn
- Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - P Schnitzler
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
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Oh DY, Biere B, Grenz M, Wolff T, Schweiger B, Dürrwald R, Reiche J. Virological Surveillance and Molecular Characterization of Human Parainfluenzavirus Infection in Children with Acute Respiratory Illness: Germany, 2015-2019. Microorganisms 2021; 9:1508. [PMID: 34361941 PMCID: PMC8307145 DOI: 10.3390/microorganisms9071508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/24/2022] Open
Abstract
Human parainfluenza viruses (HPIVs) are important causes of respiratory illness, especially in young children. However, surveillance for HPIV is rarely performed continuously, and national-level epidemiologic and genetic data are scarce. Within the German sentinel system, to monitor acute respiratory infections (ARI), 4463 respiratory specimens collected from outpatients < 5 years of age between October 2015 and September 2019 were retrospectively screened for HPIV 1-4 using real-time PCR. HPIV was identified in 459 (10%) samples. HPIV-3 was the most common HPIV-type, with 234 detections, followed by HPIV-1 (113), HPIV-4 (61), and HPIV-2 (49). HPIV-3 was more frequently associated with age < 2 years, and HPIV-4 was more frequently associated with pneumonia compared to other HPIV types. HPIV circulation displayed distinct seasonal patterns, which appeared to vary by type. Phylogenetic characterization clustered HPIV-1 in Clades 2 and 3. Reclassification was performed for HPIV-2, provisionally assigning two distinct HPIV-2 groups and six clades, with German HPIV-2s clustering in Clade 2.4. HPIV-3 clustered in C1, C3, C5, and, interestingly, in A. HPIV-4 clustered in Clades 2.1 and 2.2. The results of this study may serve to inform future approaches to diagnose and prevent HPIV infections, which contribute substantially to ARI in young children in Germany.
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Affiliation(s)
- Djin-Ye Oh
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Barbara Biere
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Markus Grenz
- Consultant Laboratory for RSV, PIV and HMPV, Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Thorsten Wolff
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Brunhilde Schweiger
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Ralf Dürrwald
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Janine Reiche
- Consultant Laboratory for RSV, PIV and HMPV, Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
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8
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Yu JM, Fu YH, Peng XL, Zheng YP, He JS. Genetic diversity and molecular evolution of human respiratory syncytial virus A and B. Sci Rep 2021; 11:12941. [PMID: 34155268 PMCID: PMC8217232 DOI: 10.1038/s41598-021-92435-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial viruses (RSVs) are classified into two major groups (A and B) based on antigenic differences in the G glycoprotein. To investigate circulating characteristics and phylodynamic history of RSV, we analyzed the genetic variability and evolutionary pattern of RSVs from 1977 to 2019 in this study. The results revealed that there was no recombination event of intergroup. Single nucleotide polymorphisms (SNPs) were observed through the genome with the highest occurrence rate in the G gene. Five and six sites in G protein of RSV-A and RSV-B, respectively, were further identified with a strong positive selection. The mean evolutionary rates for RSV-A and -B were estimated to be 1.48 × 10–3 and 1.92 × 10–3 nucleotide substitutions/site/year, respectively. The Bayesian skyline plot showed a constant population size of RSV-A and a sharp expansion of population size of RSV-B since 2005, and an obvious decrease 5 years later, then became stable again. The total population size of RSVs showed a similar tendency to that of RSV-B. Time-scaled phylogeny suggested a temporal specificity of the RSV-genotypes. Monitoring nucleotide changes and analyzing evolution pattern for RSVs could give valuable insights for vaccine and therapy strategies against RSV infection.
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Affiliation(s)
- Jie-Mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yuan-Hui Fu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Xiang-Lei Peng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yan-Peng Zheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
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9
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Korsun N, Angelova S, Trifonova I, Voleva S, Grigorova I, Tzotcheva I, Mileva S, Alexiev I, Perenovska P. Predominance of ON1 and BA9 genotypes of respiratory syncytial virus (RSV) in Bulgaria, 2016-2018. J Med Virol 2021; 93:3401-3411. [PMID: 32779756 DOI: 10.1002/jmv.26415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/07/2020] [Accepted: 08/06/2020] [Indexed: 11/06/2022]
Abstract
The objectives of this study were to investigate the prevalence of respiratory syncytial virus (RSV) infections in Bulgaria, to characterize the genetic diversity of the RSV strains, and to perform amino acid sequence analysis of the RSV G protein. Clinical, epidemiological data and nasopharyngeal swabs were prospectively collected from children aged less than 5 years presenting with acute respiratory infections from October 2016 to September 2018. Real-time polymerase chain reaction for 12 respiratory viruses, and sequencing, phylogenetic, and amino acid analyses of the RSV G gene/protein were performed. Of the 875 children examined, 645 (73.7%) were positive for at least one viral respiratory pathogen. RSV was the most commonly detected virus (26.2%), followed by rhinoviruses (15%), influenza A (H3N2) (9.7%), adenoviruses (9%), bocaviruses (7.2%), human metapneumovirus (6.1%), parainfluenza viruses 1/2/3 (5.8%), influenza type B (5.5%), and A(H1N1)pdm09 (3.4%). The detection rate for RSV varied across two winter seasons (36.7% vs 20.3%). RSV-B cases outnumbered those of the RSV-A throughout the study period. RSV was the most common virus detected in patients with bronchiolitis (45.1%) and pneumonia (24%). Phylogenetic analysis indicated that all the sequenced RSV-A strains belonged to the ON1 genotype and the RSV-B strains were classified as BA9 genotype. Amino acid substitutions at 15 and 22 positions of the HVR-2 were identified compared with the ON1 and BA prototype strains, respectively. This study revealed the leading role of RSV as a causative agent of serious respiratory illnesses in early childhood, year-on-year fluctuations in RSV incidence, the dominance of RSV-B, and relatively low genetic diversity in the circulating RSV strains.
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Affiliation(s)
- Neli Korsun
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Svetla Angelova
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivelina Trifonova
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Silvia Voleva
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iliana Grigorova
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iren Tzotcheva
- Pediatric Clinic, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
| | - Sirma Mileva
- Pediatric Clinic, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
| | - Ivaylo Alexiev
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Penka Perenovska
- Pediatric Clinic, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
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Komoyo GF, Yambiyo BM, Manirakiza A, Gody JC, Muller CP, Hübschen JM, Nakoune E, Snoeck CJ. Epidemiology and genetic characterization of respiratory syncytial virus in children with acute respiratory infections: Findings from the influenza sentinel surveillance network in Central African Republic, 2015 to 2018. Health Sci Rep 2021; 4:e298. [PMID: 34013070 PMCID: PMC8112815 DOI: 10.1002/hsr2.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND AND AIMS Respiratory syncytial virus (RSV) is one of the main viral pathogens causing acute respiratory infections in children under 5 years of age but has seldom been studied in Central African Republic (CAF). Taking advantage of the national influenza surveillance network in CAF, this study aimed at providing the first insights into RSV prevalence and seasonality over 4 years of surveillance and the clinical manifestations of RSV in this population in CAF. METHODS A total of 3903 children under 5 years matching the influenza-like illness (ILI, 68.5%) or severe acute respiratory infection (SARI, 31.5%) case definitions were recruited from January 2015 to December 2018. The presence of RSV viral RNA in nasopharyngeal samples was assessed by RT-PCR, followed by RSV-A and RSV-B typing and Sanger sequencing on a subset of samples. Phylogenetic analyses were carried on partial G protein sequences. Associations between RSV and demographic or clinical manifestations were investigated by statistical analyses. RESULTS RSV prevalence was significantly higher in infants <6 months (13.4%), in hospitalized children (13.3% vs 5.5%) and in male patients (9.5% vs 6.4%). An overall prevalence of RSV of 8.0% in the period of 2015 to 2018 was shown, with significant annual (6.4%-10.6%) and seasonal (12.7% in rainy season vs 3.0% in dry season) fluctuations. While RSV seasons in 2015, 2016, and 2018 were relatively similar, 2017 showed deviations from the overall patterns with significantly higher RSV circulation and an outbreak peak 3 to 5 months earlier. Concomitant circulation of RSV-A and RSV-B with an alternating predominance of RSV-A and RSV-B strains and temporal RSV-A genotype replacement from NA1 to ON1 was observed. CONCLUSION This study represents the first in-depth epidemiological analysis of RSV in CAF and provides first insights into RSV genetic diversity and seasonality in the country.
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Affiliation(s)
- Giscard F. Komoyo
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
- Ecole Doctorale d'Infectiologie Tropicale de Franceville, GabonFrancevilleGabon
| | - Brice M. Yambiyo
- Service d'épidémiologieInstitut Pasteur de BanguiBanguiCentral African Republic
| | | | - Jean C. Gody
- Complexe pédiatrique de BanguiCentre National Hospitalier Universitaire de BanguiBanguiCentral African Republic
| | - Claude P. Muller
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Judith M. Hübschen
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Emmanuel Nakoune
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
| | - Chantal J. Snoeck
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
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11
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Fall A, Elawar F, Hodcroft EB, Jallow MM, Toure CT, Barry MA, Kiori DE, Sy S, Diaw Y, Goudiaby D, Niang MN, Dia N. Genetic diversity and evolutionary dynamics of respiratory syncytial virus over eleven consecutive years of surveillance in Senegal. INFECTION GENETICS AND EVOLUTION 2021; 91:104864. [PMID: 33866019 DOI: 10.1016/j.meegid.2021.104864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Amary Fall
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Farah Elawar
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Mamadou Malado Jallow
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Cheikh Talibouya Toure
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Mamadou A Barry
- Unit Epidemiology of Infectious Diseases, Institute Pasteur of Dakar, Senegal.
| | | | - Sara Sy
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Yague Diaw
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | | | | | - Ndongo Dia
- Virology Department, Institute Pasteur of Dakar, Senegal.
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Mazet JAK, Genovese BN, Harris LA, Cranfield M, Noheri JB, Kinani JF, Zimmerman D, Bahizi M, Mudakikwa A, Goldstein T, Gilardi KVK. Human Respiratory Syncytial Virus Detected in Mountain Gorilla Respiratory Outbreaks. ECOHEALTH 2020; 17:449-460. [PMID: 33345293 PMCID: PMC7750032 DOI: 10.1007/s10393-020-01506-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
Respiratory illness (RI) accounts for a large proportion of mortalities in mountain gorillas (Gorilla beringei beringei), and fatal outbreaks, including disease caused by human metapneumovirus (HMPV) infections, have heightened concern about the risk of human pathogen transmission to this endangered species, which is not only critically important to the biodiversity of its ecosystem but also to the economies of the surrounding human communities. Our goal was to conduct a molecular epidemiologic study to detect the presence of HRSV and HMPV in fecal samples from wild human-habituated free-ranging mountain gorillas in Rwanda and to evaluate the role of these viruses in RI outbreaks. Fecal samples were collected from gorillas with clinical signs of RI between June 2012 and February 2013 and tested by real-time and conventional polymerase chain reaction (PCR) assays; comparison fecal samples were obtained from gorillas without clinical signs of RI sampled during the 2010 Virunga gorilla population census. PCR assays detected HMPV and HRSV first in spiked samples; subsequently, HRSV-A, the worldwide-circulating ON1 genotype, was detected in 12 of 20 mountain gorilla fecal samples collected from gorillas with RI during outbreaks, but not in samples from animals without respiratory illness. Our findings confirmed that pathogenic human respiratory viruses are transmitted to gorillas and that they are repeatedly introduced into mountain gorilla populations from people, attesting to the need for stringent biosecurity measures for the protection of gorilla health.
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Affiliation(s)
- Jonna A K Mazet
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA.
| | - Brooke N Genovese
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
| | - Laurie A Harris
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
| | - Michael Cranfield
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Davis, CA, USA
| | - Jean Bosco Noheri
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Musanze, Rwanda
| | - Jean Felix Kinani
- One Health Approach for Conservation, Gorilla Health, Kigali, Rwanda
| | - Dawn Zimmerman
- National Zoological Park, SCBI Global Health Program, Washington, DC, USA
| | - Methode Bahizi
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Musanze, Rwanda
| | | | - Tracey Goldstein
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
| | - Kirsten V K Gilardi
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Davis, CA, USA
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13
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Razanajatovo Rahombanjanahary NH, Rybkina K, Randriambolamanantsoa TH, Razafimanjato H, Heraud JM. Genetic diversity and molecular epidemiology of respiratory syncytial virus circulated in Antananarivo, Madagascar, from 2011 to 2017: Predominance of ON1 and BA9 genotypes. J Clin Virol 2020; 129:104506. [PMID: 32585620 DOI: 10.1016/j.jcv.2020.104506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND Respiratory syncytial virus is the main cause of acute respiratory infections leading to a considerable morbidity and mortality among under-5 years children. A comprehensive scheme of RSV virus evolution is of great value in implementing effective universal RSV vaccine. OBJECTIVE We investigated the clinical spectrum and molecular characteristics of detected RSV over a period of seven years (January 2011 to June 2017) in Antananarivo, the capital city of Madagascar. STUDY DESIGN 671 nasopharyngeal samples taken from children aged less than 5 years suffered from ARI were screened for RSV by real-time PCR. Clinical data were retrieved from case report forms. Genotype identification was performed by reverse-transcription PCR and sequencing of the second hyper variable region (HVR2) of the G glycoprotein. RESULTS Amongst samples tested, 292 (43.5 %) were found positive for RSV. RSV A predominated during the study period which accounted for 62.3 % (182/292) of positive samples while RSV B represented 37.0 % (108/292). Phylogenetic analyses identified NA1 and ON1 genotypes among RSV A. Though NA1 widespread from 2011 to 2013, ON1 became prevalent during the following years. Among RSV B, THB, CB1 and BA9 genotypes were detected. A co-circulation of THB and CB1 strains occurred during the 2011 season that was substituted by the BA9 from 2012. Malagasy ON1 strains carried some characteristic amino acid substitutions that distinguish them from the worldwide ON1 strains. By analyzing clinical spectrum, ON1 and BA genotypes seemed to prevail in mild infections compared to NA1. CONCLUSION Results obtained here will have its implication in predicting temporal evolution of RSV at the local level. Considering the insularity of the country, information obtained should help in comparative analysis with global RSV strains to optimize vaccine efficacy.
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Affiliation(s)
| | - Ksenia Rybkina
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Helisoa Razafimanjato
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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Systematic Review of the Respiratory Syncytial Virus (RSV) Prevalence, Genotype Distribution, and Seasonality in Children from the Middle East and North Africa (MENA) Region. Microorganisms 2020; 8:microorganisms8050713. [PMID: 32403364 PMCID: PMC7284433 DOI: 10.3390/microorganisms8050713] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most common viruses to infect children worldwide and is the leading cause of lower respiratory tract illness (LRI) in infants. This study aimed to conduct a systematic review by collecting and reviewing all the published knowledge about the epidemiology of RSV in the Middle East and North Africa (MENA) region. Therefore, we systematically searched four databases; Embase, Medline, Scopus, and Cochrane databases from 2001 to 2019 to collect all the information related to the RSV prevalence, genotype distribution, and seasonality in children in MENA region. Our search strategy identified 598 studies, of which 83 met our inclusion criteria, which cover the past 19 years (2000–2019). Odds ratio (OR) and confidence interval (CI) were calculated to measure the association between RSV prevalence, gender, and age distribution. An overall prevalence of 24.4% (n = 17,106/69,981) of respiratory infections was recorded for RSV. The highest RSV prevalence was reported in Jordan (64%, during 2006–2007) and Israel (56%, 2005–2006). RSV A subgroup was more prevalent (62.9%; OR = 2.9, 95%CI = 2.64–3.13) than RSV B. RSV was most prevalent in children who were less than 12 months old (68.6%; OR = 4.7, 95%CI = 2.6–8.6) and was higher in males (59.6%; OR = 2.17, 95%CI = 1.2–3.8) than in female infants. Finally, the highest prevalence was recorded during winter seasons in all countries, except for Pakistan. RSV prevalence in the MENA region is comparable with the global one (24.4% vs. 22%). This first comprehensive report about RSV prevalence in the MENA region and our data should be important to guide vaccine introduction decisions and future evaluation.
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15
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Palani N, Sistla S. Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 - A sentinel surveillance report from union territory of Puducherry, India. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2020; 8:1225-1235. [PMID: 32346655 PMCID: PMC7187823 DOI: 10.1016/j.cegh.2020.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/22/2020] [Indexed: 12/29/2022] Open
Abstract
Background Acute respiratory infections (ARI) are the most common illnesses affecting people of all ages worldwide. Viruses contribute to 30–70% of acute respiratory infections. Identification of these respiratory viruses is not given high priority except influenza; however, the knowledge about prevalence of non-influenza viruses, their seasonal pattern and genetic evolution have significant epidemiological value. Methods As a part of National Influenza-like illness surveillance programme, respiratory specimens were collected children and adults with symptoms of ILI or ARI, between January 2012 and March 2015 (including SARI cases). Real-time PCR was done to identify 13 respiratory viruses. Sequencing was done for representative isolates of each virus using ABI 3730 Genetic Analyzer. Results During the study period between January 2012 and March 2015, a total of 648 patients with symptoms of ARI were included in this study. The mean age of the patients was 20.2 years (SD = 19.13, median = 18); 292 (45.1%) were children (≤13 years) and 356 (54.9%) were adults. Respiratory viruses were identified in 44% (287/648) of all patients. Influenza accounted for the maximum number of cases- 179/648 (27.6%). Among the non-influenza viruses, RSV predominated with 34 cases (5.2%), followed by HMPV 24 (3.7%) and PIV-3 20 (3%). Four patients died due to INF A/H1N1 (2012-2, 2015-2) as a result of acute respiratory distress syndrome (ARDS) (CFR 3.7%). Among the non-influenza viruses, no particular seasonality pattern was observed over the different months of the study period. Conclusion Antibiotic usage in treating acute respiratory infections empirically is not justified as nearly half of ARI are due to viruses; nearly 28% of them were due to influenza viruses. Among the non-influenza viruses, RSV predominated, followed by HMPV. This study is based on an active influenza surveillance initiated after 2009 pandemic influenza outbreak, in the Union territory of Puducherry which has contributed significantly to the knowledge of the burden of influenza and non-influenza viruses among children and adults. Such surveillance network has paved the way for better diagnosis and timely therapeutic interventions. First data on the epidemiology of respiratory viruses from this region after 1974. First study to report corona virus, HCoV OC43 from India, and only the second Indian study to document corona virus, HCoV229E. This study is the first study to analyse the genetic sequence of HCoV-229E and OC-43. Influenza accounted for the maximum number of cases in the study population, 27%; four patients died of Acute respiratory distress syndrome (ARDS) due to influenza A/H1N1; CFR- 3.7%. Among the non-influenza viruses, RSV pre-dominated followed HMPV and PIV-3. No deaths were reported due to non-influenza viral ARI. RSV was detected almost equally in adults and children. Distinct pattern was observed in seasonality of influenza viruses but not for non-influenza viruses.
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Affiliation(s)
- Nandhini Palani
- National Reference Laboratory for Tuberculosis, National Institute for Research in Tuberculosis, 600031, Chennai, India
| | - Sujatha Sistla
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, 605006, Puducherry, India
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Zurita-Cruz J, Gutierrez-Gonzalez A, Manuel-Apolinar L, Fernández-Gárate JE, Arellano-Flores ML, Correa Gonzalez RA, Vázquez-Rosales G, Pérez Vieyra P, Sanchez-Armas R, Cisneros-González N. The Impact of a History of Pre-maturity on Viral Respiratory Infections in Children Under 2 Years of Age: A Propensity Score-Matching Analysis of in-hospital Complications and Mortality. Front Pediatr 2020; 8:499013. [PMID: 33072667 PMCID: PMC7531324 DOI: 10.3389/fped.2020.499013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 08/13/2020] [Indexed: 10/27/2022] Open
Abstract
Introduction: A history of pre-maturity may be a risk factor for complications in patients under 24 months of age hospitalized for viral respiratory infections (VRIs). Objective: To identify the impact of a history of pre-maturity on in-hospital complications and mortality in patients under 24 months of age who were hospitalized for VRIs over a period of 5 years. Material and Methods: This was a propensity score-matched study. The database was compiled by physicians, electronically validated by engineers, and analyzed by statisticians. Patients diagnosed with VRIs (based on International Classification of Diseases [ICD-10]) codes B974, J12, J120-J129X, J168, J17, J171, J178, J20, J203-J209, J21, J210, J211, J218, J219, J22X, and J189) from 2013 to 2017 were enrolled in the study. The subjects were classified into two groups according to the absence or presence of a history of pre-maturity (P070, P072, P073). Patients with congenital heart disease (CHD) (Q20-Q26) were excluded. Length of hospital stay, in-hospital complications, surgical procedures, and mortality were analyzed. Statistical Analysis: Patients were matched according to age. For comparisons between groups, Student's t-tests and chi2 tests were applied. A logistic regression model was constructed to identify factors related to in-hospital complications and mortality. Results: In total, 5,880 patients were eligible for inclusion in the analysis. The average patient age was 14.25 weeks. The presence of pre-maturity (coefficient = 1.16), male sex, bronchopulmonary dysplasia (BPD), in-hospital infectious complications (coefficient = 11.31), and invasive medical procedures (coefficient = 18.4) increased the number of days of hospitalization. Invasive medical procedures (OR = 6.13), a history of pre-maturity (OR = 2.54), and male sex (OR = 1.78) increased the risk for in-hospital complications. In-hospital infectious complications (OR = 84.2) and invasive medical procedures (OR = 58.4) were risk factors for mortality. Conclusions: A history of pre-maturity increased the length of hospital stay and the rate of in-hospital complications but did not increase mortality in patients under 24 months of age hospitalized for VRIs.
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Affiliation(s)
- Jessie Zurita-Cruz
- Facultad de Medicina Universidad Nacional de México, Hospital Infantil de México Federico Gómez, Unit of Research in Medical Nutrition, Pediatric Hospital "Centro Médico Nacional Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Leticia Manuel-Apolinar
- Endocrine Research Unit, Centro Médico Nacional, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | | | | | - Patricia Pérez Vieyra
- Unit of Inhalation Therapy, Pediatric Hospital, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rocio Sanchez-Armas
- Unit of Research in Medical Nutrition, Pediatric Hospital "Centro Médico Nacional Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Nelly Cisneros-González
- Epidemiological Surveillance Coordination, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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17
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Muñoz-Escalante JC, Comas-García A, Bernal-Silva S, Robles-Espinoza CD, Gómez-Leal G, Noyola DE. Respiratory syncytial virus A genotype classification based on systematic intergenotypic and intragenotypic sequence analysis. Sci Rep 2019; 9:20097. [PMID: 31882808 PMCID: PMC6934736 DOI: 10.1038/s41598-019-56552-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022] Open
Abstract
Respiratory syncytial virus (RSV), a leading cause of lower respiratory tract infections, is classified in two major groups (A and B) with multiple genotypes within them. Continuous changes in spatiotemporal distribution of RSV genotypes have been recorded since the identification of this virus. However, there are no established criteria for genotype definition, which affects the understanding of viral evolution, immunity, and development of vaccines. We conducted a phylogenetic analysis of 4,353 RSV-A G gene ectodomain sequences, and used 1,103 complete genome sequences to analyze the totallity of RSV-A genes. Intra- and intergenotype p-distance analysis and identification of molecular markers associated to specific genotypes were performed. Our results indicate that previously reported genotypes can be classified into nine distinct genotypes: GA1-GA7, SAA1, and NA1. We propose the analysis of the G gene ectodomain with a wide set of reference sequences of all genotypes for an accurate genotype identification.
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Affiliation(s)
- Juan Carlos Muñoz-Escalante
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Andreu Comas-García
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
- Center for Research in Biomedicine and Health Sciences, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Sofía Bernal-Silva
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
- Center for Research in Biomedicine and Health Sciences, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | | | - Guillermo Gómez-Leal
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Daniel E Noyola
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
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Joyce MG, Bao A, Chen M, Georgiev IS, Ou L, Bylund T, Druz A, Kong WP, Peng D, Rundlet EJ, Van Galen JG, Wang S, Yang Y, Zhang B, Chuang GY, McLellan JS, Graham BS, Mascola JR, Kwong PD. Crystal Structure and Immunogenicity of the DS-Cav1-Stabilized Fusion Glycoprotein From Respiratory Syncytial Virus Subtype B. Pathog Immun 2019; 4:294-323. [PMID: 31893251 PMCID: PMC6922093 DOI: 10.20411/pai.v4i2.338] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/21/2019] [Indexed: 11/23/2022] Open
Abstract
Background: Respiratory syncytial virus (RSV) subtypes, A and B, co-circulate in annual epidemics and alternate in dominance. We have shown that a subtype A RSV fusion (F) glycoprotein, stabilized in its prefusion conformation by DS-Cav1 mutations, is a promising RSV-vaccine immunogen, capable of boosting RSV-neutralizing titers in healthy adults. In both humans and vaccine-tested animals, neutralizing titers elicited by this subtype A DS-Cav1 immunogen were ~ 2- to 3-fold higher against the homologous subtype A virus than against the heterologous subtype B virus. Methods: To understand the molecular basis for this subtype difference, we introduced DS-Cav1 mutations into RSV strain B18537 F, determined the trimeric crystal structure, and carried out immunogenicity studies. Results: The B18537 DS-Cav1 F structure at 2-Å resolution afforded a precise delineation of prefusion F characteristics, including those of antigenic site Ø, a key trimer-apex site. Structural comparison with the subtype A prefusion F indicated 11% of surface residues to be different, with an alpha-carbon root-mean-square deviation (RMSD) of 1.2 Å; antigenic site Ø, however, differed in 23% of its surface residues and had an alpha-carbon RMSD of 2.2 Å. Immunization of vaccine-tested animals with DS-Cav1-stabilized B18537 F induced neutralizing responses ~100-fold higher than with postfusion B18537 F. Notably, elicited responses neutralized RSV subtypes A and B at similar levels and were directed towards both conserved equatorial and diverse apical regions. Conclusion: We propose that structural differences in apical and equatorial sites–coupled to differently focused immune responses–provide a molecular explanation for observed differences in elicited subtype A and B neutralizing responses.
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Affiliation(s)
- M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Amy Bao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Dongjun Peng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Emily J Rundlet
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Joseph G Van Galen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jason S McLellan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Farrag MA, Amer HM, Aziz IM, Alsaleh AN, Almajhdi FN. The emergence of subgenotype ON-1 of Human orthopneumovirus type A in Riyadh, Saudi Arabia: A new episode of the virus epidemiological dynamic. J Med Virol 2019; 92:1133-1140. [PMID: 31777964 DOI: 10.1002/jmv.25643] [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: 07/20/2019] [Accepted: 11/25/2019] [Indexed: 12/28/2022]
Abstract
Lower respiratory tract infections caused by Human orthopneumovirus are still a threat to the pediatric population worldwide. To date, the molecular epidemiology of the virus in Saudi Arabia has not been adequately charted. In this study, a total of 205 nasopharyngeal aspirate samples were collected from hospitalized children with lower respiratory tract symptoms during the winter seasons of 2014/15 and 2015/16. Human orthopneumovirus was detected in 89 (43.4%) samples, of which 56 (27.3%) were positive for type A and 33 (16.1%) were positive for type B viruses. The fragment that spans the two hypervariable regions (HVR1 and HVR2) of the G gene of Human orthopneumovirus A was amplified and sequenced. Sequence and phylogenetic analyses have revealed a genotype shift from NA1 to ON-1, which was prevalent during the winter seasons of 2007/08 and 2008/09. Based on the intergenotypic p-distance values, ON-1 was reclassified as a subgenotype of the most predominant genotype GA2. Three conserved N-glycosylation sites were observed in the HVR2 of Saudi ON-1 strains. The presence of a 23 amino acid duplicated region in ON-1 strains resulted in a higher number of O-glycosylation sites as compared to other genotypes. The data presented in this report outlined the replacement of NA1 and NA2 subgenotypes in Saudi Arabia with ON-1 within 7 to 8 years. The continuous evolution of Human orthopneumovirus through point mutations and nucleotide duplication may explain its ability to cause recurrent infections.
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Affiliation(s)
- Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Haitham M Amer
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Ibrahim M Aziz
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Asma N Alsaleh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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20
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Mollers M, Barnadas C, Broberg EK, Penttinen P, Teirlinck AC, Fischer TK. Current practices for respiratory syncytial virus surveillance across the EU/EEA Member States, 2017. Euro Surveill 2019; 24:1900157. [PMID: 31595876 PMCID: PMC6784450 DOI: 10.2807/1560-7917.es.2019.24.40.1900157] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BackgroundRespiratory syncytial virus (RSV) is a major contributor to lower respiratory tract infections worldwide and several vaccine candidates are currently in development. Following vaccine introduction, reliable RSV surveillance should enable monitoring of vaccination impact. Data on the RSV disease burden in the European Union and European Economic Area (EU/EEA) are sparse.AimThe aim of this study was to gather knowledge on current practices of national RSV surveillance in the EU/EEA.MethodsNational Coordinators and National Focal Points for Influenza (epidemiologists and virologists) from the EU/EEA countries (n = 31) were invited to participate in an online survey in August and September 2017. The questionnaire covered questions on epidemiological and laboratory aspects of RSV surveillance.ResultsAll EU/EEA countries except Liechtenstein replied to the survey. Eighteen countries reported to have a sentinel surveillance system, 26 countries a non-sentinel surveillance system and three countries to have neither. RSV data collection was mostly done within the context of influenza surveillance. A wide range of diagnostic and characterisation assays was used for the detection of RSV.DiscussionThe majority of EU/EEA countries have some surveillance for RSV in place. The prevailing integration of RSV surveillance into the existing influenza sentinel surveillance system may lead to under-reporting of RSV. The documented variations in existing RSV surveillance systems and their outputs indicate that there is scope for developing guidelines on establishing comparable methods and outcomes for RSV surveillance across the EU/EEA, to ensure the availability of a consistent evidence base for assessing future vaccination programmes.
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Affiliation(s)
- Madelief Mollers
- National Institute for Public Health and the Environment (RIVM) - Centre for Infectious disease control, Bilthoven, the Netherlands,European Programme for Intervention Epidemiology Training (EPIET) and European Public Health Microbiology (EUPHEM) training programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden,These authors contributed equally to this manuscript
| | - Céline Barnadas
- European Programme for Intervention Epidemiology Training (EPIET) and European Public Health Microbiology (EUPHEM) training programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden,These authors contributed equally to this manuscript,Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Eeva K Broberg
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Pasi Penttinen
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | - Anne C Teirlinck
- National Institute for Public Health and the Environment (RIVM) - Centre for Infectious disease control, Bilthoven, the Netherlands,These authors contributed equally to this manuscript
| | - Thea K Fischer
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark,Department of Infectious Diseases and Centre for Global Health, University of Southern Denmark, Odense, Denmark,These authors contributed equally to this manuscript
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21
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Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010-2013. J Infect Public Health 2019; 13:438-445. [PMID: 31229412 DOI: 10.1016/j.jiph.2019.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Data on the viral etiology of acute lower respiratory infections are scarce in Pakistan. Human respiratory syncytial virus (RSV) is an important cause of morbidity in children but no effective vaccine or antiviral therapy is currently available. As vaccines are expected to become available in the future, it is important to understand the epidemiology of locally prevalent RSV subtypes. This study aimed to define the molecular epidemiology of RSV (A and B) genotypes in Pakistani children under 5 years. METHODS World Health Organization case definitions for influenza-like illness (ILI) and severe acute respiratory illness (SARI) were used for case selection. Children under 5 years who presented with ILI or SARI at tertiary care hospitals from all provinces/regions, including the eight influenza sentinel sites, during October-April each year between 2010 and 2013 were enrolled. Demographic and clinical data of the children were recorded and nasopharyngeal/throat swabs taken for analysis. All samples were tested for RSV A and B using real-time polymerase chain reaction for non-influenza respiratory viruses. Specific oligonucleotide primers for RSV A and B were used for subtyping and sequencing of the G protein, followed by phylogenetic analysis. RESULTS A total of 1941 samples were included. RSV was detected in 472 (24%) children, with RSV A detected in 367 (78%) and RSV B in 105 (22%). The G protein of all RSV A strains clustered in the NA1/GA2 genotype while RSV B strains carried the signature 60 nucleotide duplication and were assigned to three BA genotypes: BA-9, BA-10 and the new BA-13 genotype. CONCLUSIONS This study highlights the importance of RSV as a viral etiologic agent of acute respiratory infections in children in Pakistan, and the diversity of RSV viruses. Continued molecular surveillance for early detection of prevalent and newly emerging genotypes is needed to understand the epidemiology of RSV infections in Pakistan.
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22
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Malekshahi SS, Razaghipour S, Samieipoor Y, Hashemi FB, Manesh AAR, Izadi A, Faghihloo E, Ghavami N, Mokhtari-Azad T, Salimi V. Molecular characterization of the glycoprotein and fusion protein in human respiratory syncytial virus subgroup A: Emergence of ON-1 genotype in Iran. INFECTION GENETICS AND EVOLUTION 2019; 71:166-178. [PMID: 30946992 DOI: 10.1016/j.meegid.2019.03.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 03/05/2019] [Accepted: 03/29/2019] [Indexed: 12/20/2022]
Abstract
HRSV is a principle cause of infant hospitalization, childhood wheezing and a common pathogen in the elderly. Limited information exists regarding HRSV genotypes in Iran. In order to better understand HRSV strain diversity, we performed an in-depth evaluation of the genetic variability of the HRSV F protein detected in children under two years of age that, presented with acute respiratory symptoms during 2015-2016 in Tehran. A total of 180 nasopharyngeal swabs were evaluated. The HRSV positive samples were genotyped for G and F gene sequences using RT-PCR and sequencing methods. Phylogenetic analysis was performed using the neighbor-joining and maximum likelihood methods. Genetic and antigenic characteristics of the F gene, nucleotide and amino acids in significant positions and immune system binding regions, as well as the p-distance, positive/negative selection site, linear epitopes and glycosylation sites were investigated in all selected sequences. Among the 83 HRSV positive samples, the Fifty-five cases were successfully sequenced. All of them were classified as subgroup A and belonged to the ON-1 genotype, which possessed 72-nt duplication in the G gene. This study is the first report on the emergence of ON-1 in Iran. ON-1 Iranian sequences clustered in three lineages according to virus fusion (F) gene variations. F gene sequence analysis showed that all genetic changes in the isolates from Iran were base substitutions and no deletion/insertions were identified. The low dN/dS ratio and lack of positively selected sites showed that the fusion genes found in the strains from Iran are not under host selective pressure. Continuing and long-term molecular epidemiological surveys for early detection of circulating and newly emerging genotypes are necessary to gain a better understanding of their epidemic potential.
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Affiliation(s)
| | - Shaghayegh Razaghipour
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yazdan Samieipoor
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad B Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Anahita Izadi
- Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nastaran Ghavami
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Fritsch A, Schweiger B, Biere B. Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014. Euro Surveill 2019; 24:1800174. [PMID: 30862333 PMCID: PMC6415498 DOI: 10.2807/1560-7917.es.2019.24.10.1800174] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/31/2018] [Indexed: 11/23/2022] Open
Abstract
IntroductionRecent data on influenza C virus indicate a possible higher clinical impact in specified patient populations than previously thought.AimWe aimed to investigate influenza C virus circulation in Germany.MethodsA total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. The samples represented a subset of all samples from the German national surveillance system for influenza in this age group in 2012-14. The presence of influenza C virus was investigated by real-time PCR. For positive samples, information on symptoms as well as other respiratory virus co-infections was considered. Retrieved influenza C viral sequences were phylogenetically characterised.ResultsInfluenza C viral RNA was detected in 20 (1.3% of) samples, including 16 during the 2012/13 season. The majority (18/20) of influenza C-positive patients had ILI according to the European Union definition, one patient had pneumonia. Viruses belonged to the C/Sao Paulo and C/Kanagawa lineages. Most (11/20) samples were co-infected with other respiratory viruses.ConclusionOur data are the first on influenza C virus circulation in Germany and notably from a European national surveillance system. The low detection frequency and the identified virus variants confirm earlier observations outside a surveillance system. More virus detections during the 2012/13 season indicate a variable circulation intensity in the different years studied. Influenza C virus can be considered for ILI patients. Future studies addressing its clinical impact, especially in patients with severe disease are needed.
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Affiliation(s)
- Annemarie Fritsch
- Robert Koch Institute, National Reference Center for Influenza, FG 17 Influenza and Other Respiratory Viruses, Berlin, Germany
| | - Brunhilde Schweiger
- Robert Koch Institute, National Reference Center for Influenza, FG 17 Influenza and Other Respiratory Viruses, Berlin, Germany
| | - Barbara Biere
- Robert Koch Institute, National Reference Center for Influenza, FG 17 Influenza and Other Respiratory Viruses, Berlin, Germany
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24
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Obodai E, Odoom JK, Adiku T, Goka B, Wolff T, Biere B, Schweiger B, Reiche J. The significance of human respiratory syncytial virus (HRSV) in children from Ghana with acute lower respiratory tract infection: A molecular epidemiological analysis, 2006 and 2013-2014. PLoS One 2018; 13:e0203788. [PMID: 30199549 PMCID: PMC6130863 DOI: 10.1371/journal.pone.0203788] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Background Acute lower respiratory tract infection (ALRI) is a leading cause of childhood morbidity and mortality in developing countries. Globally, human respiratory syncytial virus (HRSV) is the most common pathogen of ALRI in infants and children. However, age-stratified HRSV disease burden data are largely absent from Africa, which is a key gap in informing an evidence-based recommendation for the introduction of an HRSV vaccine by the WHO. Methods This study investigated the presence of HRSV in respiratory specimens from 552 children <5 years old with ALRI from Accra, Ghana in 2006 and 2013–2014 by real-time PCR. Of HRSV-positive samples the second hypervariable region of the viral G protein gene was sequenced and analyzed for phylogeny, characteristic amino acid substitutions, and potential glycosylation patterns. Further, HRSV infections have been characterized by age, symptoms and timely occurrence. Results HRSV was observed in 23% (127/552) of the children with ALRI, with the highest incidence in infants younger than one year (33%, 97/295, p = 0.013). Within the observed seasonal circulation time of HRSV from June (mid-wet season) to December (beginning of the dry season) the incidence of ALRI due to HRSV was as high as 46% (125/273). HRSV disease was significantly associated with (broncho-) pneumonia, bronchiolitis, LRTI, and difficulty in breathing. Phylogenetic characterization of HRSV strains from Ghana identified the circulation of the currently worldwide prevailing genotypes ON1 and BA9, and shows evidence of an independent molecular evolution of ON1 and BA9 strains in Ghana resulting in potentially new subgenotypes within ON1 and BA9, provisionally named ON1.5, ON1.6, and BA9-IV. Conclusion This study addresses important knowledge gaps in the forefront of introducing the HRSV vaccine by providing information on the molecular evolution and incidence of HRSV in Accra (Ghana, Africa).
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Affiliation(s)
- Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
| | - John Kofi Odoom
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Theophilus Adiku
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
| | - Bamenla Goka
- Department of Child Health, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Thorsten Wolff
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Barbara Biere
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Brunhilde Schweiger
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Janine Reiche
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
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Alchikh M, Conrad T, Hoppe C, Ma X, Broberg E, Penttinen P, Reiche J, Biere B, Schweiger B, Rath B. Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care. Clin Microbiol Infect 2018; 25:380.e9-380.e16. [PMID: 29906596 DOI: 10.1016/j.cmi.2018.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 01/21/2023]
Abstract
OBJECTIVES Hospital-based surveillance of influenza and acute respiratory infections relies on International Classification of Diseases (ICD) codes and hospital laboratory reports (Standard-of-Care). It is unclear how many cases are missed with either method, i.e. remain undiagnosed/coded as influenza and other respiratory virus infections. Various influenza-like illness (ILI) definitions co-exist with little guidance on how to use them. We compared the diagnostic accuracy of standard surveillance methods with a prospective quality management (QM) programme at a Berlin children's hospital with the Robert Koch Institute. METHODS Independent from routine care, all patients fulfilling pre-defined ILI-criteria (QM-ILI) participated in the QM programme. A separate QM team conducted standardized clinical assessments and collected nasopharyngeal specimens for blinded real-time quantitative PCR for influenza A/B viruses, respiratory syncytial virus, adenovirus, rhinovirus and human metapneumovirus. RESULTS Among 6073 individuals with ILI qualifying for the QM programme, only 8.7% (528/6073) would have undergone virus diagnostics during Standard-of-Care. Surveillance based on ICD codes would have missed 61% (359/587) of influenza diagnoses. Of baseline ICD codes, 53.2% (2811/5282) were non-specific, most commonly J06 ('acute upper respiratory infection'). Comparison of stakeholder case definitions revealed that QM-ILI and the WHO ILI case definition showed the highest overall sensitivities (84%-97% and 45%-68%, respectively) and the CDC ILI definition had the highest sensitivity for influenza infections (36%, 95% CI 31.4-40.8 for influenza A and 48%, 95% CI 40.5-54.7 for influenza B). CONCLUSIONS Disease-burden estimates and surveillance should account for the underreporting of cases in routine care. Future studies should explore the effect of ILI screening and surveillance in various age groups and settings. Diagnostic algorithms should be based on the WHO ILI case definition combined with targeted testing.
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Affiliation(s)
- M Alchikh
- Department of Paediatrics, Charité University Berlin, Germany; Vienna Vaccine Safety Initiative, Berlin, Germany
| | - T Conrad
- Department of Mathematics and Computer Sciences, Freie Universität Berlin, Germany
| | - C Hoppe
- Vienna Vaccine Safety Initiative, Berlin, Germany
| | - X Ma
- Department of Paediatrics, Charité University Berlin, Germany; Vienna Vaccine Safety Initiative, Berlin, Germany; National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - E Broberg
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - P Penttinen
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - J Reiche
- National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - B Biere
- National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - B Schweiger
- National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - B Rath
- Department of Paediatrics, Charité University Berlin, Germany; Vienna Vaccine Safety Initiative, Berlin, Germany; University of Nottingham School of Medicine, Nottingham, UK.
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Swamy MA, Malhotra B, Janardhan Reddy PV, Tiwari J. Profile of Respiratory Pathogens Causing Acute Respiratory Infections in Hospitalised Children at Rajasthan a 4 Year’s Study. Indian J Med Microbiol 2018; 36:163-171. [DOI: 10.4103/ijmm.ijmm_18_84] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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27
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Bayrakdar F, Kocabas CN, Altas AB, Kavuncuoglu HG, Cosgun Y, Mısırlıoglu ED, Durmaz I, Korukluoglu G, Ozkul A. Genetic variability human respiratory syncytial virus subgroups A and B in Turkey during six successive epidemic seasons, 2009-2015. J Med Virol 2017; 90:456-463. [PMID: 29077212 PMCID: PMC7166824 DOI: 10.1002/jmv.24983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/12/2017] [Indexed: 01/10/2023]
Abstract
Human respiratory syncytial virus (HRSV) is most important viral respiratory pathogen of acute lower respiratory tract infections in infants and young children worldwide. The circulating pattern and genetic characteristics in the HRSV attachment glycoprotein gene were investigated in Turkey during six consecutive seasons from 2009 to 2015. HRSVA was dominant in the all epidemic seasons except 2011‐2012 season. Partial sequences of the HVR2 region of the G gene of 479 HRSVA and 135 HRSVB were obtained. Most Turkish strains belonged to NA1, ON1, and BA9, which were the predominant genotypes circulating worldwide. Although three novel genotypes, TR‐A, TR‐BA1, and TR‐BA2, were identified, they were not predominant. Clinical data were available for 69 HRSV‐positive patients who were monitored due to acute lower respiratory tract illness. There were no significant differences in the clinical diagnosis, hospitalization rates, laboratory findings and treatment observed between the HRSVA and HRSVB groups, and co‐infections in this study. The major population afflicted by HRSV infections included infants and children between 13 and 24 months of age. We detected that the CB1, GB5, and THB strains clustered in the same branch with a bootstrap value of 100%. CB‐B and BA12 strains clustered in the same branch with a bootstrap value of 65%. The BA11 genotype was clustered in the BA9 genotype in our study. The present study may contribute on the molecular epidemiology of HRSV in Turkey and provide data for HRSV strains circulating in local communities and other regions worldwide.
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Affiliation(s)
- Fatma Bayrakdar
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Can Naci Kocabas
- Pediatric Immunology and Allergy Unit, Faculty of Medicine, Mugla Sitki Koçman Universty, Muğla, Turkey
| | - Ayse Basak Altas
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - H Gokhan Kavuncuoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Yasemin Cosgun
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Emine Dibek Mısırlıoglu
- Department of Pediatric Allergy and Immunology, Ankara Children's Hematology Oncology Training and Research Hospital, Ankara, Turkey
| | - Ihsan Durmaz
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Aykut Ozkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey
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Köndgen S, Calvignac-Spencer S, Grützmacher K, Keil V, Mätz-Rensing K, Nowak K, Metzger S, Kiyang J, Lübke-Becker A, Deschner T, Wittig RM, Lankester F, Leendertz FH. Evidence for Human Streptococcus pneumoniae in wild and captive chimpanzees: A potential threat to wild populations. Sci Rep 2017; 7:14581. [PMID: 29109465 PMCID: PMC5674046 DOI: 10.1038/s41598-017-14769-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/11/2017] [Indexed: 11/09/2022] Open
Abstract
Habituation of wild great apes for tourism and research has had a significant positive effect on the conservation of these species. However, risks associated with such activities have been identified, specifically the transmission of human respiratory viruses to wild great apes, causing high morbidity and, occasionally, mortality. Here, we investigate the source of bacterial-viral co-infections in wild and captive chimpanzee communities in the course of several respiratory disease outbreaks. Molecular analyses showed that human respiratory syncytial viruses (HRSV) and human metapneumoviruses (HMPV) were involved in the etiology of the disease. In addition our analysis provide evidence for coinfection with Streptococcus (S.) pneumoniae. Characterisation of isolates from wild chimpanzees point towards a human origin of these bacteria. Transmission of these bacteria is of concern because - in contrast to HRSV and HMPV - S. pneumoniae can become part of the nasopharyngeal flora, contributing to the severity of respiratory disease progression. Furthermore these bacteria have the potential to spread to other individuals in the community and ultimately into the population. Targeted vaccination programs could be used to vaccinate habituated great apes but also human populations around great ape habitats, bringing health benefits to both humans and wild great apes.
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Affiliation(s)
- Sophie Köndgen
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany.,Institute of Medical Virology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | | | - Kim Grützmacher
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany
| | - Verena Keil
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany
| | | | - Kathrin Nowak
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany.,Department for Infectious Disease Epidemiology, Robert-Koch-Institute, 13353, Berlin, Germany
| | - Sonja Metzger
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103, Leipzig, Germany.,Evolutionary Ecology, Leipniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - John Kiyang
- Limbe Wildlife Centre, Limbe, SW Region, Cameroon
| | - Antina Lübke-Becker
- Berlin Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163, Berlin, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103, Leipzig, Germany
| | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, 01 BP 1303, Abidjan, Ivory Coast
| | - Felix Lankester
- Limbe Wildlife Centre, Limbe, SW Region, Cameroon.,Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
| | - Fabian H Leendertz
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany.
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Korsun N, Angelova S, Tzotcheva I, Georgieva I, Lazova S, Parina S, Alexiev I, Perenovska P. Prevalence and genetic characterisation of respiratory syncytial viruses circulating in Bulgaria during the 2014/15 and 2015/16 winter seasons. Pathog Glob Health 2017; 111:351-361. [PMID: 28948867 DOI: 10.1080/20477724.2017.1375708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The respiratory syncytial virus (RSV) is a leading cause of acute respiratory illnesses (ARI) in infants and young children. The objectives of this study were to investigate the RSV circulation among children aged <5 years in Bulgaria, to identify the RSV-A and RSV-B genotypes and to perform an amino acid sequence analysis of second hypervariable region (HVR2) of the G gene. During the 2014/15 and 2015/16 winter seasons, nasopharyngeal specimens of 610 children aged <5 years with ARI were tested using Real Time RT-PCR for influenza viruses, RSV, metapneumovirus, parainfluenza viruses, rhinoviruses and adenoviruses. Viral respiratory pathogens were detected in 429 (70%) out of 610 patients examined and RSV was the most frequently identified virus (26%) followed by influenza A(H1N1)pdm09 virus (14%) (p < .05). RSV was the most prevalent pathogen in patients with bronchiolitis (48%) and pneumonia (38%). In the 2014/15 season, RSV-A dominated slightly (53%), while in the next season RSV-B viruses prevailed more strongly (66%). The phylogenetic analysis based on the G gene indicated that all 21 studied RSV-A strains belonged to the ON1 genotype; the vast majority (96%) of the RSV-B strains were classified into BA9 genotype and only one - into BA10 genotype. All Bulgarian RSV-A and RSV-B sequences contained a 72-nt and a 60-nt duplication in the HVR2, respectively. The study showed the leading role of this pathogen as a causative agent of serious respiratory illnesses in early childhood, year-on-year fluctuations in RSV incidence, a shift from RSV-A to RSV-B subgroup dominance and relatively low genetic divergence in the circulating strains.
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Affiliation(s)
- Neli Korsun
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Svetla Angelova
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Iren Tzotcheva
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Irina Georgieva
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Snezhina Lazova
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Snezhana Parina
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Ivaylo Alexiev
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Penka Perenovska
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
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30
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Rath B, Conrad T, Myles P, Alchikh M, Ma X, Hoppe C, Tief F, Chen X, Obermeier P, Kisler B, Schweiger B. Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials. Expert Rev Anti Infect Ther 2017; 15:545-568. [PMID: 28277820 PMCID: PMC7103706 DOI: 10.1080/14787210.2017.1295847] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Influenza-Like Illness is a leading cause of hospitalization in children. Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Areas covered: We present a composite clinical score allowing individual patient data analyses of disease severity based on systematic literature review and WHO-criteria for uncomplicated and complicated disease. The 22-item ViVI Disease Severity Score showed a normal distribution in a pediatric cohort of 6073 children aged 0-18 years (mean age 3.13; S.D. 3.89; range: 0 to 18.79). Expert commentary: The ViVI Score was correlated with risk of antibiotic use as well as need for hospitalization and intensive care. The ViVI Score was used to track children with influenza, respiratory syncytial virus, human metapneumovirus, human rhinovirus, and adenovirus infections and is fully compliant with regulatory data standards. The ViVI Disease Severity Score mobile application allows physicians to measure disease severity at the point-of care thereby taking clinical trials to the next level.
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Affiliation(s)
- Barbara Rath
- a Division of Pediatric Infectious Diseases , Vienna Vaccine Safety Initiative , Berlin , Germany.,b Department of Pediatrics , Charité University Medical Center , Berlin , Germany.,c Division of Epidemiology and Public Health , University of Nottingham , Nottingham , UK
| | - Tim Conrad
- d Department of Mathematics and Computer Science , Freie Universität Berlin , Berlin , Germany
| | - Puja Myles
- c Division of Epidemiology and Public Health , University of Nottingham , Nottingham , UK
| | - Maren Alchikh
- a Division of Pediatric Infectious Diseases , Vienna Vaccine Safety Initiative , Berlin , Germany.,b Department of Pediatrics , Charité University Medical Center , Berlin , Germany
| | - Xiaolin Ma
- b Department of Pediatrics , Charité University Medical Center , Berlin , Germany.,e National Reference Centre for Influenza and Other Respiratory Viruses , Robert Koch Institute , Berlin , Germany
| | - Christian Hoppe
- a Division of Pediatric Infectious Diseases , Vienna Vaccine Safety Initiative , Berlin , Germany.,d Department of Mathematics and Computer Science , Freie Universität Berlin , Berlin , Germany
| | - Franziska Tief
- a Division of Pediatric Infectious Diseases , Vienna Vaccine Safety Initiative , Berlin , Germany.,b Department of Pediatrics , Charité University Medical Center , Berlin , Germany
| | - Xi Chen
- a Division of Pediatric Infectious Diseases , Vienna Vaccine Safety Initiative , Berlin , Germany.,b Department of Pediatrics , Charité University Medical Center , Berlin , Germany
| | - Patrick Obermeier
- a Division of Pediatric Infectious Diseases , Vienna Vaccine Safety Initiative , Berlin , Germany.,b Department of Pediatrics , Charité University Medical Center , Berlin , Germany
| | - Bron Kisler
- f Clinical Data Standards Interchange Consortium (CDISC) , Austin , TX , USA
| | - Brunhilde Schweiger
- e National Reference Centre for Influenza and Other Respiratory Viruses , Robert Koch Institute , Berlin , Germany
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31
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Swamy MA, Malhotra B, Reddy PVJ, Tiwari JK, Kumar N, Gupta ML. Trends of respiratory syncytial virus sub-types in children hospitalised at a tertiary care centre in Jaipur during 2012-2014. Indian J Med Microbiol 2017; 35:134-136. [PMID: 28303835 DOI: 10.4103/ijmm.ijmm_15_306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Respiratory syncytial virus (RSV) causes high mortality and morbidity in infants. The study was planned to determine the trends of RSV sub-types in hospitalised children. Nasopharyngeal aspirate and throat swabs were collected from the hospitalised children up to 5 years of age. Viral nucleic acid was extracted using easyMAG automated extraction system, and real-time reverse transcription polymerase chain reaction was performed. Total positivity for RSV was found to be 25.40%, predominantly for RSV B (20.03%), followed by RSV A (2.90%) and RSV AB mixed infections (2.47%). Palivizumab prophylaxis can be planned to be given to infants from post-monsoon to end of winter.
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Affiliation(s)
- M Anjaneya Swamy
- Department of Microbiology and Immunology, Advanced Basic Sciences and Clinical Research Laboratory (ICMR Grade-I Viral Diagnostics and Research Laboratory), Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Bharti Malhotra
- Department of Microbiology and Immunology, Advanced Basic Sciences and Clinical Research Laboratory (ICMR Grade-I Viral Diagnostics and Research Laboratory), Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - P V Janardhan Reddy
- Department of Microbiology and Immunology, Advanced Basic Sciences and Clinical Research Laboratory (ICMR Grade-I Viral Diagnostics and Research Laboratory), Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Jitendra Kumar Tiwari
- Department of Microbiology and Immunology, Advanced Basic Sciences and Clinical Research Laboratory (ICMR Grade-I Viral Diagnostics and Research Laboratory), Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Neeraj Kumar
- Department of Microbiology and Immunology, Advanced Basic Sciences and Clinical Research Laboratory (ICMR Grade-I Viral Diagnostics and Research Laboratory), Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Manohar Lal Gupta
- Department of Paediatrics Medicine, JK Lone Hospital, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
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32
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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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33
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Grützmacher K, Keil V, Leinert V, Leguillon F, Henlin A, Couacy-Hymann E, Köndgen S, Lang A, Deschner T, Wittig RM, Leendertz FH. Human quarantine: Toward reducing infectious pressure on chimpanzees at the Taï Chimpanzee Project, Côte d'Ivoire. Am J Primatol 2017; 80. [PMID: 28095600 PMCID: PMC7161855 DOI: 10.1002/ajp.22619] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 10/13/2016] [Accepted: 10/19/2016] [Indexed: 12/02/2022]
Abstract
Due to their genetic relatedness, great apes are highly susceptible to common human respiratory pathogens. Although most respiratory pathogens, such as human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV), rarely cause severe disease in healthy human adults, they are associated with considerable morbidity and mortality in wild great apes habituated to humans for research or tourism. To prevent pathogen transmission, most great ape projects have established a set of hygiene measures ranging from keeping a specific distance, to the use of surgical masks and establishment of quarantines. This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human‐great ape interface, the Taï Chimpanzee Project (TCP) in Côte d'Ivoire, and consequently, the effectiveness of a 5‐day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. To assess the impact of quarantine as a preventative measure, we monitored the quarantine process and tested 262 throat swabs for respiratory viruses, collected during quarantine over a period of 1 year. Although only 1 subject tested positive for a respiratory virus (HRSV), 17 subjects developed symptoms of infection while in quarantine and were subsequently kept from approaching the chimpanzees, preventing potential exposure in 18 cases. Our results suggest that quarantine—in combination with monitoring for symptoms—is effective in reducing the risk of potential pathogen exposure. This research contributes to our understanding of how endangered great apes can be protected from human‐borne infectious disease.
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Affiliation(s)
- Kim Grützmacher
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany.,Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Verena Keil
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
| | - Vera Leinert
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Floraine Leguillon
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany.,University Montpellier 2, Montpellier, France
| | - Arthur Henlin
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany.,University Montpellier 2, Montpellier, France
| | - Emmanuel Couacy-Hymann
- Laboratoire National d'appui au Développement Agricole/Laboratoire Central de Pathologie Animale, Bingerville, Côte d'Ivoire
| | - Sophie Köndgen
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
| | - Alexander Lang
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
| | - Tobias Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, CSRS, Abidjan, Côte d'Ivoire
| | - Fabian H Leendertz
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
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34
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Bashir U, Nisar N, Mahmood N, Alam MM, Sadia H, Zaidi SSZ. Molecular detection and characterization of respiratory syncytial virus B genotypes circulating in Pakistani children. INFECTION GENETICS AND EVOLUTION 2016; 47:125-131. [PMID: 27908797 DOI: 10.1016/j.meegid.2016.11.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 10/20/2022]
Abstract
Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infections in young children, but very little is known about its epidemiology and circulating genotypes in Pakistan. This study analyzed the epidemiological and molecular characteristics of RSV B genotypes in Pakistani children below 5years with acute respiratory tract infections (ARIs) during three consecutive winter seasons from 2010 to 2013. A total of 1941 samples were analyzed for RSV infection by real time PCR and 24% (472/1941) samples were found positive out of which 22.3% (105/472) were sub-typed as RSV-B. The frequency of outpatient cases was higher (62.5%; 295/472) as compared to hospitalized patients (37.5%; 177/472). Patient ages ranged from 2month to 5years with a mean age of 1.48±1.2 (years) and a median age of 1year. Children below one year made up the highest percentage of enrolled subjects and male to female ratio of RSVB positive cases was nearly equivalent (1:1.1). The most common clinical symptoms were cough (96%), fever (80%) and sore throat (50%). All Pak RSVB strains ascribed to the BA genotype showing 91.9-97.1% and 86.2-95.3% homology at the nucleotide and amino acid levels respectively in comparison to BA prototype strain. On phylogenetic analysis, three genotypes of Pakistan RSV B viruses were observed; BA-9 and BA-10 which have been reported previously from other regions, and a third novel genotype assigned as BA-13 which formed a distinct cluster with protein length of 319 AA and showed 9-11 unique AA substitutions. All the RSV B isolates had two potential N-glycosylation sites in HVR2 of G protein and with heavy O-glycosylation of serine and threonine residues (G scores of 0.5-0.7). This study highlights the diversity of RSVB viruses and the significance of RSV as a dominant viral etiologic agent of pediatric ARI. It also emphasizes the need for continued molecular surveillance for early detection of prevalent and newly emerging genotypes to understand epidemiology of RSV infections in various regions of Pakistan.
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Affiliation(s)
- Uzma Bashir
- Atta-Ur-Rahman School of Applied Sciences, National University of Sciences and Technology, Islamabad, Pakistan; Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Nadia Nisar
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Nayab Mahmood
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Muhammad Masroor Alam
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Hajra Sadia
- Atta-Ur-Rahman School of Applied Sciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
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35
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Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014. PLoS One 2016; 11:e0166145. [PMID: 27835664 PMCID: PMC5106011 DOI: 10.1371/journal.pone.0166145] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/23/2016] [Indexed: 01/10/2023] Open
Abstract
Respiratory syncytial virus (RSV) is an important viral pathogen of acute respiratory tract infection (ARI). Limited data are available on molecular epidemiology of RSV from Saudi Arabia. A total of 130 nasopharyngeal aspirates were collected from children less than 5 years of age with ARI symptoms attending the Emergency Department at King Khalid University Hospital and King Fahad Medical City, Riyadh, Saudi Arabia between October and December, 2014. RSV was identified in the 26% of the hospitalized children by reverse transcriptase PCR. Group A RSV (77%) predominated during the study as compared to group B RSV (23%). The phylogenetic analysis of 28 study strains clustered group A RSV in NA1 and ON1 genotypes and group B viruses in BA (BA9) genotype. Interestingly, 26% of the positive samples clustered in genotypes with duplication in the G protein gene (ON1 for group A and BA for group B). Both the genotypes showed enhanced O-linked glycosylation in the duplicated region, with 10 and 2 additional sites in ON1 and BA respectively. Selection pressure analysis revealed purifying selection in both the ON1 and BA genotypes. One codon each in the ON1 (position 274) and BA genotypes (position 219) were positively selected and had high entropy values indicating variations at these amino acid positions. This is the first report describing the presence of ON1 genotype and the first report on co-circulation of two different genotypes of RSV with duplication in the G protein gene from Saudi Arabia. The clinical implications of the simultaneous occurrence of genotypes with duplication in G protein gene in a given population especially in the concurrent infections should be investigated in future. Further, the ongoing surveillance of RSV in this region will reveal the evolutionary trajectory of these two genotypes with duplication in G protein gene from largest country in the Middle East.
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36
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Calderón A, Pozo F, Calvo C, García-García M, González-Esguevillas M, Molinero M, Casas I. Genetic variability of respiratory syncytial virus A in hospitalized children in the last five consecutive winter seasons in Central Spain. J Med Virol 2016; 89:767-774. [PMID: 27696460 DOI: 10.1002/jmv.24703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 12/18/2022]
Abstract
Human respiratory syncytial virus group A (RSV-A) was detected in symptomatic hospital attended children in Central Spain for a continuous time period, September 2010 to April 2015. In order to accurately describe the epidemiology of this virus, the genetic diversity of the complete G gene and the clinical manifestations observed were jointly analyzed. Out of 3,011 respiratory specimens taken from 2,308 children, 640 were positive to RSV (21.3%) and 405 were RSV-A (63.2%). Complete G gene sequences of 166 randomly selected RSV-A virus identified NA1 and ON1 genotypes. In 2011-2012, ON1 emerged sporadically and become dominant in 2012-2013 with 38 cases (70%). In 2014-2015, all the 44 sequences contained the 72-nt duplication (100%). Clinical diagnosis of children with ON1 genotype were bronchiolitis in 55 (62.5%), recurrent wheezing or asthma exacerbations in 22 (25%), laryngotracheobronchitis in 3 (3.4%), and upper respiratory tract infections in eight. Results showed replacement and substitution of circulating NA1 genotype with the new ON1 genotype. Nevertheless, at this stage, none of the RSV-A genotypes identified have resulted in significant clinical differences. The amino acid composition of the complete G gene ON1 sequences demonstrated an accumulation of single changes not related with different clinical presentation. J. Med. Virol. 89:767-774, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ana Calderón
- Respiratory Virus and Influenza Unit, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Pozo
- Respiratory Virus and Influenza Unit, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Mónica González-Esguevillas
- Respiratory Virus and Influenza Unit, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Molinero
- Respiratory Virus and Influenza Unit, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
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37
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Grützmacher KS, Köndgen S, Keil V, Todd A, Feistner A, Herbinger I, Petrzelkova K, Fuh T, Leendertz SA, Calvignac-Spencer S, Leendertz FH. Codetection of Respiratory Syncytial Virus in Habituated Wild Western Lowland Gorillas and Humans During a Respiratory Disease Outbreak. ECOHEALTH 2016; 13:499-510. [PMID: 27436109 PMCID: PMC7088376 DOI: 10.1007/s10393-016-1144-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 05/11/2023]
Abstract
Pneumoviruses have been identified as causative agents in several respiratory disease outbreaks in habituated wild great apes. Based on phylogenetic evidence, transmission from humans is likely. However, the pathogens have never been detected in the local human population prior to or at the same time as an outbreak. Here, we report the first simultaneous detection of a human respiratory syncytial virus (HRSV) infection in western lowland gorillas (Gorilla gorilla gorilla) and in the local human population at a field program in the Central African Republic. A total of 15 gorilla and 15 human fecal samples and 80 human throat swabs were tested for HRSV, human metapneumovirus, and other respiratory viruses. We were able to obtain identical sequences for HRSV A from four gorillas and four humans. In contrast, we did not detect HRSV or any other classic human respiratory virus in gorilla fecal samples in two other outbreaks in the same field program. Enterovirus sequences were detected but the implication of these viruses in the etiology of these outbreaks remains speculative. Our findings of HRSV in wild but human-habituated gorillas underline, once again, the risk of interspecies transmission from humans to endangered great apes.
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Affiliation(s)
- Kim S Grützmacher
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Seestr 10, 13353, Berlin, Germany
| | - Sophie Köndgen
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Seestr 10, 13353, Berlin, Germany
| | - Verena Keil
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Seestr 10, 13353, Berlin, Germany
| | - Angelique Todd
- World Wildlife Fund (WWF), Dzanga Sangha Protected Areas, Bayanga, Central African Republic
| | - Anna Feistner
- World Wildlife Fund (WWF), Dzanga Sangha Protected Areas, Bayanga, Central African Republic
| | | | - Klara Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences, Brno, 60365, Czech Republic
- Biology Centre, Institute of Parasitology, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic
| | - Terrence Fuh
- World Wildlife Fund (WWF), Dzanga Sangha Protected Areas, Bayanga, Central African Republic
| | - Siv Aina Leendertz
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Seestr 10, 13353, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Seestr 10, 13353, Berlin, Germany
| | - Fabian H Leendertz
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Seestr 10, 13353, Berlin, Germany.
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Saxena S, Singh D, Zia A, Umrao J, Srivastava N, Pandey A, Singh S, Bhattacharya P, Kumari R, Kushwaha R, Dhole TN. Clinical characterization of influenza A and human respiratory syncytial virus among patients with influenza like illness. J Med Virol 2016; 89:49-54. [PMID: 27329816 DOI: 10.1002/jmv.24607] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 06/04/2016] [Accepted: 06/20/2016] [Indexed: 01/30/2023]
Abstract
Influenza A and Respiratory Syncytial Virus (RSV) has been recognized as a major cause of acute respiratory tract infection. H1N1 is one of the subtypes of influenza A, pandemic worldwide in July 2009, causing 18,449 deaths globally. To investigate the prevalence and clinical manifestation of the influenza A, H1N1pdm09, and RSV. Throat/nasal swab collected from the patients of all age group either outpatients/inpatients having respiratory illness from 2 to 5 days. The clinical data were recorded in a predesigned questionnaire. RNA was extracted and analyzed by real time PCR at a tertiary care center, 2009-2014. Total 4,352 samples tested for influenza A and H1N1. Out of 4,352, 32.2% (median positivity 21%; range 16-41% during 6 years) were positive for influenza A and 19% were H1N1 (median positivity 16.7%; range 8.7-23% during 6 years). Total 1653 samples were analyzed for RSV from 2011 to 2014, 12% were RSV positive (median positivity 11.35%; range 10-16.3% during 4 years). Pharyngitis, dyspnea were frequent symptoms in influenza A and H1N1 (P < 0.005) whereas bronchiolitis and pneumonia were commonly present in RSV (P < 0.005). The positivity of influenza A and H1N1 was higher in age-group 21-30, whereas RSV in infant and children. H1N1 and RSV were co-circulated and have common clinical symptoms particularly in lower age group. Therefore, laboratory confirmation is necessary for further disease prognosis. Age was an important risk factor that affects the positivity of influenza A, H1N1, and RSV. Different clinical manifestation of H1N1 and RSV will be helpful for early and accurate diagnosis. J. Med. Virol. 89:49-54, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Swati Saxena
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India.,Chhatrapati Shahuji Maharaj Medical University, Lucknow, U.P., India
| | - Dharamveer Singh
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India
| | - Amreen Zia
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India
| | - Jyoti Umrao
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India
| | - Naveen Srivastava
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India
| | - Ankita Pandey
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India
| | - Sushma Singh
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India
| | - Piyali Bhattacharya
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India
| | - Reema Kumari
- Chhatrapati Shahuji Maharaj Medical University, Lucknow, U.P., India
| | - Ramawadh Kushwaha
- Chhatrapati Shahuji Maharaj Medical University, Lucknow, U.P., India
| | - T N Dhole
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, U.P., India.
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Hu P, Zheng T, Chen J, Zhou T, Chen Y, Xu X, Pei X. Alternate circulation and genetic variation of human respiratory syncytial virus genotypes in Chengdu, West China, 2009-2014. J Med Virol 2016; 89:32-40. [PMID: 27322084 DOI: 10.1002/jmv.24603] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2016] [Indexed: 11/05/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a major pathogen that causes worldwide seasonal epidemic disease in infants due to its genetic variations. However, published information on the molecular epidemiology of HRSV was never reported particularly in Chengdu of West China. During five consecutive seasons (from 2009 to 2014), 433 (23.7%) of 1827 samples from hospitalized patients were identified as HRSV positive. Epidemiological characteristics of HRSV revealed that subtype A viruses (62.7%) prevailed in the first three epidemic seasons and faded in the next two seasons, while subtype B viruses (37.3%) kept circulating in five epidemic periods. According to the phylogenetic analysis of glycoprotein (G) gene, five HRSV genotypes NA1, ON1, BA9, BA-C, and CB1 were found in Chengdu. The predominant circulating genotype changed from NA1 in the period of 2010-2012 to BA9 of 2013-2014. The newly emerging ON1 was first reported in West China in October 2013. The early genotypes BA-C and CB1 were replaced by the prevailing BA9 after the third epidemic peak. Genetic mutations in glycosylation sites of G protein were found in HRSV variants, suggesting the virus is able to escape the immune recognition and attack. This study elucidated the local HRSV epidemic was associated with the alternate circulation of multiple genotypes and with the change of glycosylation sites of G protein. J. Med. Virol. 89:32-40, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Pengwei Hu
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China.,Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Tianli Zheng
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Jiayi Chen
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Tao Zhou
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Yuhang Chen
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xin Xu
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xiaofang Pei
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China.
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Tief F, Hoppe C, Seeber L, Obermeier P, Chen X, Karsch K, Mühlhans S, Adamou E, Conrad T, Beresniak A, Schweiger B, Adam T, Rath B. An inception cohort study assessing the role of pneumococcal and other bacterial pathogens in children with influenza and ILI and a clinical decision model for stringent antibiotic use. Antivir Ther 2016; 21:413-24. [PMID: 26867096 DOI: 10.3851/imp3034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Influenza-like illness (ILI) is a common reason for paediatric consultations. Viral causes predominate, but antibiotics are used frequently. With regard to influenza, pneumococcal coinfections are considered major contributors to morbidity/mortality. METHODS In the context of a perennial quality management (QM) programme at the Charité Departments of Paediatrics and Microbiology in collaboration with the Robert Koch Institute, children aged 0-18 years presenting with signs and symptoms of ILI were followed from the time of initial presentation until hospital discharge (Charité Influenza-Like Disease = ChILD Cohort). An independent QM team performed highly standardized clinical assessments using a disease severity score based on World Health Organization criteria for uncomplicated and complicated/progressive disease. Nasopharyngeal and pharyngeal samples were collected for viral reverse transcription polymerase chain reaction and bacterial culture/sensitivity and MaldiTOF analyses. The term 'detection' was used to denote any evidence of viral or bacterial pathogens in the (naso)pharyngeal cavity. With the ChILD Cohort data collected, a standard operating procedure (SOP) was created as a model system to reduce the inappropriate use of antibiotics in children with ILI. Monte Carlo simulations were performed to assess cost-effectiveness. RESULTS Among 2,569 ChILD Cohort patients enrolled from 12/2010 to 04/2013 (55% male, mean age 3.2 years, range 0-18, 19% >5 years), 411 patients showed laboratory-confirmed influenza, with bacterial co-detection in 35%. Influenza and pneumococcus were detected simultaneously in 12/2,569 patients, with disease severity clearly below average. Pneumococcal vaccination rates were close to 90%. Nonetheless, every fifth patient was already on antibiotics upon presentation; new antibiotic prescriptions were issued in an additional 20%. Simulation of the model SOP in the same dataset revealed that the proposed decision model could have reduced the inappropriate use of antibiotics significantly (P<0.01) with an incremental cost-effectiveness ratio of -99.55€. CONCLUSIONS Physicians should be made aware that in times of pneumococcal vaccination the prevalence and severity of influenza infections complicated by pneumococci may decline. Microbiological testing in combination with standardized disease severity assessments and review of vaccination records could be cost-effective, as well as promoting stringent use of antibiotics and a personalized approach to managing children with ILI.
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Affiliation(s)
- Franziska Tief
- Department of Paediatrics, Charité University Medical Centre Berlin, Berlin, Germany
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Long-Term Shedding of Influenza Virus, Parainfluenza Virus, Respiratory Syncytial Virus and Nosocomial Epidemiology in Patients with Hematological Disorders. PLoS One 2016; 11:e0148258. [PMID: 26866481 PMCID: PMC4750950 DOI: 10.1371/journal.pone.0148258] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/15/2016] [Indexed: 01/25/2023] Open
Abstract
Respiratory viruses are a cause of upper respiratory tract infections (URTI), but can be associated with severe lower respiratory tract infections (LRTI) in immunocompromised patients. The objective of this study was to investigate the genetic variability of influenza virus, parainfluenza virus and respiratory syncytial virus (RSV) and the duration of viral shedding in hematological patients. Nasopharyngeal swabs from hematological patients were screened for influenza, parainfluenza and RSV on admission as well as on development of respiratory symptoms. Consecutive swabs were collected until viral clearance. Out of 672 tested patients, a total of 111 patients (17%) were infected with one of the investigated viral agents: 40 with influenza, 13 with parainfluenza and 64 with RSV; six patients had influenza/RSV or parainfluenza/RSV co-infections. The majority of infected patients (n = 75/111) underwent stem cell transplantation (42 autologous, 48 allogeneic, 15 autologous and allogeneic). LRTI was observed in 48 patients, of whom 15 patients developed severe LRTI, and 13 patients with respiratory tract infection died. Phylogenetic analysis revealed a variety of influenza A(H1N1)pdm09, A(H3N2), influenza B, parainfluenza 3 and RSV A, B viruses. RSV A was detected in 54 patients, RSV B in ten patients. The newly emerging RSV A genotype ON1 predominated in the study cohort and was found in 48 (75%) of 64 RSV-infected patients. Furthermore, two distinct clusters were detected for RSV A genotype ON1, identical RSV G gene sequences in these patients are consistent with nosocomial transmission. Long-term viral shedding for more than 30 days was significantly associated with prior allogeneic transplantation (p = 0.01) and was most pronounced in patients with RSV infection (n = 16) with a median duration of viral shedding for 80 days (range 35–334 days). Long-term shedding of respiratory viruses might be a catalyzer of nosocomial transmission and must be considered for efficient infection control in immunocompromised patients.
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Tuan TA, Thanh TT, Hai NTT, Tinh LBB, Kim LTN, Do LAH, Chinh B'Krong NTT, Tham NT, Hang VTT, Merson L, Farrar J, Thuong TC, de Jong MD, Schultsz C, van Doorn HR. Characterization of hospital and community-acquired respiratory syncytial virus in children with severe lower respiratory tract infections in Ho Chi Minh City, Vietnam, 2010. Influenza Other Respir Viruses 2016; 9:110-9. [PMID: 25702707 PMCID: PMC4415695 DOI: 10.1111/irv.12307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is an important community and nosocomial pathogen in developed countries but data regarding the importance of RSV in developing countries are relatively scarce. METHODS During a 1-year surveillance study in 2010, we took serial samples from children admitted to the Emergency Unit of the Respiratory Ward of Children's Hospital 1 in Ho Chi Minh City, Vietnam. RSV was detected within 72 hours of admission to the ward in 26% (376/1439; RSV A: n = 320; RSV B: n = 54; and RSV A and B: n = 2). Among those negative in the first 72 hours after admission, 6.6% (25/377) acquired nosocomial RSV infection during hospitalization (RSV A: n = 22; and RSV B: n = 3). RESULTS Children with nosocomial RSV infection were younger (P = 0.001) and had a longer duration of hospitalization (P < 0.001). The rate of incomplete recovery among children with nosocomial RSV infection was significantly higher than among those without (P < 0.001). Phylogenetic analysis of partial G gene sequences obtained from 79% (316/401) of positive specimens revealed the co-circulation of multiple genotypes with RSV A NA1 being predominant (A NA1: n = 275; A GA5: n = 5; B BA3: n = 3; B BA9: n = 26; and B BA10: n = 7). The RSV A GA5 and RSV B BA3 genotypes have not been reported from Vietnam, previously. CONCLUSION Besides emphasizing the importance of RSV as a cause of respiratory infection leading to hospitalization in young children and as a nosocomial pathogen, data from this study extend our knowledge on the genetic diversity of RSV circulating in Vietnam.
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Yu X, Kou Y, Xia D, Li J, Yang X, Zhou Y, He X. Human respiratory syncytial virus in children with lower respiratory tract infections or influenza-like illness and its co-infection characteristics with viruses and atypical bacteria in Hangzhou, China. J Clin Virol 2015. [PMID: 26209367 PMCID: PMC7185398 DOI: 10.1016/j.jcv.2015.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is the most important viral pathogen in children. However, its epidemic patterns and co-infection characteristics are not fully understood. OBJECTIVES We attempted to determine the level of genetic variation of RSV, and describe the prevalence and co-infection characteristics of RSV in Hangzhou during two epidemic seasons. STUDY DESIGN Single respiratory samples from 1820 pediatric patients were screened for RSV and genotyped by RT-PCR and sequencing. In all RSV positive specimens, we screened for viruses and atypical bacteria. Demographic and clinical information was recorded and analyzed. RESULTS A total of 34.5% and 3.8% of samples from acute lower respiratory tract infections (ALRI) and influenza-like illness (ILI) were positive for RSV, respectively. Phylogenetic analysis revealed that 61.1% of the selected 167 RSV strains were NA1, 31.1% were BA, 3.6% were ON1, 2.4% were CB1, and 1.8% were NA3. A new genotype, BA11 was identified, which comprised 98.1% of BA strains in this study, while the rest were BA10. A total of 36.4% and 9.1% of RSV-positive children with ALRI and ILI respectively were found to be co-infected. Rhinovirus was the most common additional respiratory virus, followed by human metapneumovirus. Except for fever, no significant differences in other clinical presentation between the RSV mono-infection and co-infection groups were observed. CONCLUSIONS The circulating RSV strains had high genetic variability with RSV-B showing a more local pattern. In ALRI cases, co-infection of RSV with other viruses or atypical bacteria has no significant effect on the clinical presentation except fever.
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Affiliation(s)
- Xinfen Yu
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China.
| | - Yu Kou
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Daozong Xia
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jun Li
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Xuhui Yang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Yinyan Zhou
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaoyan He
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
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44
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Molecular epidemiology and molecular characterization of respiratory syncytial viruses at a tertiary care university hospital in Catalonia (Spain) during the 2013–2014 season. J Clin Virol 2015; 66:27-32. [DOI: 10.1016/j.jcv.2015.02.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/22/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023]
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45
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Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes. PLoS One 2015; 10:e0120098. [PMID: 25793751 PMCID: PMC4368745 DOI: 10.1371/journal.pone.0120098] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/19/2015] [Indexed: 11/19/2022] Open
Abstract
Background Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relatively few whole genome sequences are available for RSV. The goal of our study was to sequence the genomes of RSV strains collected from multiple countries to further understand the global diversity of RSV at a whole-genome level. Methods We collected RSV samples and isolates from Mexico, Argentina, Belgium, Italy, Germany, Australia, South Africa, and the USA from the years 1998-2010. Both Sanger and next-generation sequencing with the Illumina and 454 platforms were used to sequence the whole genomes of RSV A and B. Phylogenetic analyses were performed using the Bayesian and maximum likelihood methods of phylogenetic inference. Results We sequenced the genomes of 34 RSVA and 23 RSVB viruses. Phylogenetic analysis showed that the RSVA genome evolves at an estimated rate of 6.72 × 10-4 substitutions/site/year (95% HPD 5.61 × 10-4 to 7.6 × 10-4) and for RSVB the evolutionary rate was 7.69 × 10-4 substitutions/site/year (95% HPD 6.81 × 10-4 to 8.62 × 10-4). We found multiple clades co-circulating globally for both RSV A and B. The predominant clades were GA2 and GA5 for RSVA and BA for RSVB. Conclusions Our analyses showed that RSV circulates on a global scale with the same predominant clades of viruses being found in countries around the world. However, the distribution of clades can change rapidly as new strains emerge. We did not observe a strong spatial structure in our trees, with the same three main clades of RSV co-circulating globally, suggesting that the evolution of RSV is not strongly regionalized.
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Evaluation of novel second-generation RSV and influenza rapid tests at the point of care. Diagn Microbiol Infect Dis 2014; 81:171-6. [PMID: 25583129 DOI: 10.1016/j.diagmicrobio.2014.11.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/27/2014] [Accepted: 11/24/2014] [Indexed: 11/23/2022]
Abstract
Acute respiratory infections represent common pediatric emergencies. Infection control warrants immediate and accurate diagnoses. In the past, first-generation respiratory syncytial virus (RSV) rapid tests (strip tests) have shown suboptimal sensitivities. In 2013, the Food and Drug Administration licensed a second-generation RSV rapid test providing user-independent readouts (SOFIA™-RSV) using automated fluorescence assay technology known to yield superior results with influenza rapid testing. We are reporting the first point-of-care evaluation of the SOFIA™-RSV rapid test. In the Charité Influenza-Like Disease Cohort, 686 nasopharyngeal samples were tested in parallel with SOFIA™-RSV and SOFIA™-Influenza A+B. Compared to real-time PCR, SOFIA™-RSV sensitivities/specificities were 78.6%/93.9%, respectively (SOFIA™-Influenza A: 80.6%/99.3%). Performance was greatest in patients below 2 years of age with a test sensitivity of 81.8%. RSV sensitivities were highest (85%) in the first 2 days of illness and with nasopharyngeal compared to nasal swabs (P=0.055, McNemar's test). Second-generation RSV and influenza rapid testing provides highly accurate results facilitating timely patient cohortation and management.
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47
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Kim YI, DeVincenzo JP, Jones BG, Rudraraju R, Harrison L, Meyers R, Cehelsky J, Alvarez R, Hurwitz JL. Respiratory syncytial virus human experimental infection model: provenance, production, and sequence of low-passaged memphis-37 challenge virus. PLoS One 2014; 9:e113100. [PMID: 25415360 PMCID: PMC4240712 DOI: 10.1371/journal.pone.0113100] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 10/19/2014] [Indexed: 01/11/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children and is responsible for as many as 199,000 childhood deaths annually worldwide. To support the development of viral therapeutics and vaccines for RSV, a human adult experimental infection model has been established. In this report, we describe the provenance and sequence of RSV Memphis-37, the low-passage clinical isolate used for the model's reproducible, safe, experimental infections of healthy, adult volunteers. The predicted amino acid sequences for major proteins of Memphis-37 are compared to nine other RSV A and B amino acid sequences to examine sites of vaccine, therapeutic, and pathophysiologic interest. Human T- cell epitope sequences previously defined by in vitro studies were observed to be closely matched between Memphis-37 and the laboratory strain RSV A2. Memphis-37 sequences provide baseline data with which to assess: (i) virus heterogeneity that may be evident following virus infection/transmission, (ii) the efficacy of candidate RSV vaccines and therapeutics in the experimental infection model, and (iii) the potential emergence of escape mutants as a consequence of experimental drug treatments. Memphis-37 is a valuable tool for pre-clinical research, and to expedite the clinical development of vaccines, therapeutic immunomodulatory agents, and other antiviral drug strategies for the protection of vulnerable populations against RSV disease.
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Affiliation(s)
- Young-In Kim
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Children's Foundation Research Institute of Le Bonheur Children's Hospital, Memphis, Tennessee, United States of America
| | - John P. DeVincenzo
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Children's Foundation Research Institute of Le Bonheur Children's Hospital, Memphis, Tennessee, United States of America
| | - Bart G. Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Rajeev Rudraraju
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Lisa Harrison
- Children's Foundation Research Institute of Le Bonheur Children's Hospital, Memphis, Tennessee, United States of America
| | - Rachel Meyers
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Jeff Cehelsky
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Rene Alvarez
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Julia L. Hurwitz
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
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Tabatabai J, Prifert C, Pfeil J, Grulich-Henn J, Schnitzler P. Novel respiratory syncytial virus (RSV) genotype ON1 predominates in Germany during winter season 2012-13. PLoS One 2014; 9:e109191. [PMID: 25290155 PMCID: PMC4188618 DOI: 10.1371/journal.pone.0109191] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 08/29/2014] [Indexed: 11/19/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of hospitalization especially in young children with respiratory tract infections (RTI). Patterns of circulating RSV genotypes can provide a better understanding of the molecular epidemiology of RSV infection. We retrospectively analyzed the genetic diversity of RSV infection in hospitalized children with acute RTI admitted to University Hospital Heidelberg/Germany between October 2012 and April 2013. Nasopharyngeal aspirates (NPA) were routinely obtained in 240 children younger than 2 years of age who presented with clinical symptoms of upper or lower RTI. We analyzed NPAs via PCR and sequence analysis of the second variable region of the RSV G gene coding for the attachment glycoprotein. We obtained medical records reviewing routine clinical data. RSV was detected in 134/240 children. In RSV-positive patients the most common diagnosis was bronchitis/bronchiolitis (75.4%). The mean duration of hospitalization was longer in RSV-positive compared to RSV-negative patients (3.5 vs. 5.1 days; p<0.01). RSV-A was detected in 82.1%, RSV-B in 17.9% of all samples. Phylogenetic analysis of 112 isolates revealed that the majority of RSV-A strains (65%) belonged to the novel ON1 genotype containing a 72-nucleotide duplication. However, genotype ON1 was not associated with a more severe course of illness when taking basic clinical/laboratory parameters into account. Molecular characterization of RSV confirms the co-circulation of multiple genotypes of subtype RSV-A and RSV-B. The duplication in the G gene of genotype ON1 might have an effect on the rapid spread of this emerging RSV strain.
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Affiliation(s)
- Julia Tabatabai
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christiane Prifert
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Johannes Pfeil
- Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
- German Centre for Infectious Diseases (DZIF), Heidelberg, Germany
| | | | - Paul Schnitzler
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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Pierangeli A, Trotta D, Scagnolari C, Ferreri ML, Nicolai A, Midulla F, Marinelli K, Antonelli G, Bagnarelli P. Rapid spread of the novel respiratory syncytial virus A ON1 genotype, central Italy, 2011 to 2013. Euro Surveill 2014; 19. [DOI: 10.2807/1560-7917.es2014.19.26.20843] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Respiratory infections positive for human respiratory syncytial virus (RSV) subtype A were characterised in children admitted to hospitals in Rome and Ancona (Italy) over the last three epidemic seasons. Different strains of the novel RSV-A genotype ON1, first identified in Ontario (Canada) in December 2010, were detected for the first time in Italy in the following 2011/12 epidemic season. They bear an insertion of 24 amino acids in the G glycoprotein as well as amino acid changes likely to change antigenicity. By early 2013, ON1 strains had spread so efficiently that they had nearly replaced other RSV-A strains. Notably, the RSV peak in the 2012/13 epidemic season occurred earlier and, compared with the previous two seasons, influenza-like illnesses diagnoses were more frequent in younger children; bronchiolitis cases had a less severe clinical course. Nonetheless, the ON1-associated intensive care unit admission rate was similar, if not greater, than that attributable to other RSV-A strains. Improving RSV surveillance would allow timely understanding of the epidemiological and clinicopathological features of the novel RSV-A genotype.
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Affiliation(s)
- A Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - D Trotta
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
| | - C Scagnolari
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - M L Ferreri
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
| | - A Nicolai
- Department of Paediatrics, Sapienza University, Rome, Italy
| | - F Midulla
- Department of Paediatrics, Sapienza University, Rome, Italy
| | - K Marinelli
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
| | - G Antonelli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - P Bagnarelli
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
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Cai XY, Wang Q, Lin GY, Cai ZW, Lin CX, Chen PZ, Zhou XH, Xie JC, Lu XD. Respiratory virus infections among children in South China. J Med Virol 2014; 86:1249-55. [PMID: 24619492 DOI: 10.1002/jmv.23931] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2014] [Indexed: 02/05/2023]
Abstract
Acute respiratory tract infection is an important cause of morbidity and mortality with a worldwide disease burden. This study aimed to determine the prevalence and clinical characteristics of children with viral-induced acute respiratory tract infection, in Southern China. Nasopharyngeal aspirate samples from 1,980 pediatric patients with suspected acute respiratory tract infection, and 82 samples from healthy subject controls were collected for routine examination at the Second Affiliated Hospital of Shantou University Medical College, from October 2007 to August 2011. Specimens were tested by multiplex polymerase chain reaction (mPCR). At least one or more viruses were detected from 1,087 samples (54.9%). These included laboratory confirmations for 446 respiratory syncytial virus (RSV), 386 influenza virus A (FluA), 315 human rhinovirus (HRV), 135 human bocavirus (HBoV), 119 Parainfluenza virus 3 (PIV3), 82 Parainfluenza virus 1 (PIV1), 66 adenovirus (ADV), 53 WU polyomavirus (WUPyV), 52 human metapneumovirus (hMPV), and 29 influenza virus B (FluB) samples. Samples from healthy subjects were negative for any virus. Of the patients with positive specimens, 107 (9.8%) were admitted to pediatric intensive care unit (PICU). Co-infection with at least two of the viral pathogens under study was observed in 325 of the 1,980 patients (16.4% of the total number of cases). These findings may help in the diagnosis of viral infections of the respiratory tract in children, and help to consider current and potential therapeutic approaches for the treatment of acute respiratory tract infection, and further respiratory complications.
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Affiliation(s)
- Xiao-Ying Cai
- Department of Pediatrics, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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