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Verwey C, Dangor Z, Madhi SA. Approaches to the Prevention and Treatment of Respiratory Syncytial Virus Infection in Children: Rationale and Progress to Date. Paediatr Drugs 2024; 26:101-112. [PMID: 38032456 PMCID: PMC10891269 DOI: 10.1007/s40272-023-00606-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection (LRTI) in children, and is associated with long-term pulmonary sequelae for up to 30 years after infection. The mainstay of RSV management is supportive therapy such as supplemental oxygen. Palivizumab (Synagis™-AstraZeneca), a monoclonal antibody targeting the RSV F protein site II, has been licensed for the prevention of RSV in high-risk groups since 1998. There has been recent promising progress in preventative strategies that include vaccines and long-acting, high-potency monoclonal antibodies. Nirsevimab (Beyfortus™-AstraZeneca/Sanofi), a monoclonal antibody with an extended half-life, has recently been registered in the European Union and granted licensure by the US Food and Drug Administration. Furthermore, a pre-fusion sub-unit protein vaccine has been granted licensure for pregnant women, aimed at protecting their young infants, following established safety and efficacy in clinical trials (Abrysvo™-Pfizer). Also, multiple novel antiviral therapeutic options are in early phase clinical trials. The next few years have the potential to change the landscape of LRTI through improvements in the prevention and management of RSV LRTI. Here, we discuss these new approaches, current research, and clinical trials in novel therapeutics, monoclonal antibodies, and vaccines against RSV infection in infants and children.
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Affiliation(s)
- Charl Verwey
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ziyaad Dangor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Verwey C, Madhi SA. Review and Update of Active and Passive Immunization Against Respiratory Syncytial Virus. BioDrugs 2023; 37:295-309. [PMID: 37097594 PMCID: PMC10127166 DOI: 10.1007/s40259-023-00596-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 04/26/2023]
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection (LRTI) in children, causing approximately 3.6 million hospitalizations per year, and has been associated with long-term pulmonary sequelae for up to 30 years after infection, yet preventative strategies and active treatment options remain elusive. The associated morbidity and healthcare related costs could be decreased substantially with the development of these much-needed medications. After an initial false start in the development of an RSV vaccine, gradual progress is now being made with the development of multiple vaccine candidates using numerous different mechanisms of action. Furthermore, nirsevimab, a new monoclonal antibody for the prevention of RSV, has recently been registered in the European Union. New novel treatments for RSV infection are also in the pipeline, which would provide the clinician with much needed ammunition in the management of the acute disease. The next few years have the potential to change the landscape of LRTI forever through the prevention and management of RSV LRTI and thereby decrease the mortality and morbidity associated with it. In this review, we discuss these new approaches, current research, and clinical trials in monoclonal antibody and vaccine development against RSV.
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Affiliation(s)
- Charl Verwey
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise (ALIVE), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Kim HN, Hwang J, Yoon SY, Lim CS, Cho Y, Lee CK, Nam MH. Molecular characterization of human respiratory syncytial virus in Seoul, South Korea, during 10 consecutive years, 2010-2019. PLoS One 2023; 18:e0283873. [PMID: 37023101 PMCID: PMC10079039 DOI: 10.1371/journal.pone.0283873] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/19/2023] [Indexed: 04/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections and hospitalization in infants and young children. Here, we analyzed the genetic diversity of RSV using partial G gene sequences in 84 RSV-A and 78 RSV- B positive samples collected in Seoul, South Korea, for 10 consecutive years, from 2010 to 2019. Our phylogenetic analysis revealed that RSV-A strains were classified into either the ON1 (80.9%) or NA1 (19.0%) genotypes. On the other hand, RSV-B strains demonstrated diversified clusters within the BA genotype. Notably, some sequences designated as BA-SE, BA-SE1, and BA-DIS did not cluster with previously identified BA genotypes in the phylogenetic trees. Despite this, they did not meet the criteria for the assignment of a new genotype based on recent classification methods. Selection pressure analysis identified three positive selection sites (amino acid positions 273, 274, and 298) in RSV-A, and one possible positive selection site (amino acid position 296) in RSV-B, respectively. The mean evolutionary rates of Korean RSV-A from 1999 to 2019 and RSV-B strains from 1991 and 2019 were estimated at 3.51 × 10-3 nucleotides (nt) substitutions/site/year and 3.32 × 10-3 nt substitutions/site/year, respectively. The population dynamics in the Bayesian skyline plot revealed fluctuations corresponding to the emergence of dominant strains, including a switch of the dominant genotype from NA1 to ON1. Our study on time-scaled cumulative evolutionary analysis contributes to a better understanding of RSV epidemiology at the local level in South Korea.
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Affiliation(s)
- Ha Nui Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Jinha Hwang
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Soo-Young Yoon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chang-Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
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ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia. Genes (Basel) 2022; 13:genes13122288. [PMID: 36553555 PMCID: PMC9778264 DOI: 10.3390/genes13122288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.
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Lin TY, Chi H, Kuo CY, Tsai HP, Wang JR, Liu CC, Shen CF. Outbreak of respiratory syncytial virus subtype ON1 among children during COVID-19 pandemic in Southern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1168-1179. [PMID: 36137926 DOI: 10.1016/j.jmii.2022.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND The regional respiratory syncytial virus (RSV) outbreak in southern Taiwan in late 2020 followed the surge of RSV cases in the national surveillance data and displayed distinct clinical features. This study investigated RSV epidemiology in the most recent five years and compared the clinical manifestations of this outbreak with non-outbreak period. METHODS Medical records of RSV-infected children at the National Cheng Kung University Hospital from January 2016 to December 2020 were retrospectively retrieved from hospital-based electronic medical database. Cases of RSV infection were identified by RSV antigen positive and/or RSV isolated from respiratory specimens. The demographic, clinical presentations, and laboratory data were recorded. The RSV isolates in 2020 was sequenced for phylogenetic analysis. RESULTS Overall, 442 RSV-infected cases were retrieved and 42.1% (186 cases) clustered in late 2020. The 2020 outbreak started in September, peaked in November, and lasted for 3 months. 2020 RSV-infected children were older (2.3 ± 2.2 years vs. 1.0 ± 1.0 years), more likely to be diagnosed with bronchopneumonia (57.5% vs. 31.6%), but also had a lower hospitalization rate, shorter hospital stay, less oxygen use, and less respiratory distress than those in 2016-2019 (all p value < 0.05). The RSV isolates in 2020 belonged to RSV-A subtype ON1 but were phylogenetically distinct from the ON1 strains prevalent in Taiwan previously. CONCLUSION The 2020 RSV outbreak was led by the novel RSV-A subtype ON1 variant with clinical manifestations distinct from previous years. Continuous surveillance of new emerging variants of respiratory viruses in the post-pandemic era is warranted.
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Affiliation(s)
- Ting-Yu Lin
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin Chi
- Department of Medicine, MacKay Medicine College, New Taipei, Taiwan; Department of Pediatrics, MacKay Children's Hospital and MacKay Memorial Hospital, Taipei, Taiwan
| | - Cheng-Yen Kuo
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.
| | - Ching-Fen Shen
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Rios Guzman E, Hultquist JF. Clinical and biological consequences of respiratory syncytial virus genetic diversity. Ther Adv Infect Dis 2022; 9:20499361221128091. [PMID: 36225856 PMCID: PMC9549189 DOI: 10.1177/20499361221128091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most common etiological agents of global acute respiratory tract infections with a disproportionate burden among infants, individuals over the age of 65, and immunocompromised populations. The two major subtypes of RSV (A and B) co-circulate with a predominance of either group during different epidemic seasons, with frequently emerging genotypes due to RSV's high genetic variability. Global surveillance systems have improved our understanding of seasonality, disease burden, and genomic evolution of RSV through genotyping by sequencing of attachment (G) glycoprotein. However, the integration of these systems into international infrastructures is in its infancy, resulting in a relatively low number (~2200) of publicly available RSV genomes. These limitations in surveillance hinder our ability to contextualize RSV evolution past current canonical attachment glycoprotein (G)-oriented understanding, thus resulting in gaps in understanding of how genetic diversity can play a role in clinical outcome, therapeutic efficacy, and the host immune response. Furthermore, utilizing emerging RSV genotype information from surveillance and testing the impact of viral evolution using molecular techniques allows us to establish causation between the clinical and biological consequences of arising genotypes, which subsequently aids in informed vaccine design and future vaccination strategy. In this review, we aim to discuss the findings from current molecular surveillance efforts and the gaps in knowledge surrounding the consequence of RSV genetic diversity on disease severity, therapeutic efficacy, and RSV-host interactions.
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Affiliation(s)
- Estefany Rios Guzman
- Department of Medicine, Division of Infectious
Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL,
USA
- Center for Pathogen Genomics and Microbial
Evolution, Institute for Global Health, Northwestern University Feinberg
School of Medicine, Chicago, IL, USA
| | - Judd F. Hultquist
- Robert H. Lurie Medical Research Center,
Northwestern University, 9-141, 303 E. Superior St., Chicago, IL 60611,
USA
- Department of Medicine, Division of Infectious
Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL,
USA
- Center for Pathogen Genomics and Microbial
Evolution, Institute for Global Health, Northwestern University Feinberg
School of Medicine, Chicago, IL, USA
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Zhang Z, Ma P, Ahmed R, Wang J, Akin D, Soto F, Liu BF, Li P, Demirci U. Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2103646. [PMID: 34623709 DOI: 10.1002/adma.202103646] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/25/2021] [Indexed: 04/14/2023]
Abstract
The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.
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Affiliation(s)
- Zhaowei Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Peng Ma
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Rajib Ahmed
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Jie Wang
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Demir Akin
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Fernando Soto
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Peiwu Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
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Rahman F, Libre C, Oleinikov A, Tcherniuk S. Chloroquine and pyrimethamine inhibit the replication of human respiratory syncytial virus A. J Gen Virol 2021; 102. [PMID: 34342560 DOI: 10.1099/jgv.0.001627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human respiratory syncytial virus (hRSV) is a major cause of respiratory illness in young children and can cause severe infections in the elderly or in immunocompromised adults. To date, there is no vaccine to prevent hRSV infections, and disease management is limited to preventive care by palivizumab in infants and supportive care for adults. Intervention with small-molecule antivirals specific for hRSV represents a good alternative, but no such compounds are currently approved. The investigation of existing drugs for new therapeutic purposes (drug repositioning) can be a faster approach to address this issue. In this study, we show that chloroquine and pyrimethamine inhibit the replication of human respiratory syncytial virus A (long strain) and synergistically increase the anti-replicative effect of ribavirin in cellulo. Moreover, chloroquine, but not pyrimethamine, inhibits hRSV replication in the mouse model. Our results show that chloroquine can potentially be an interesting compound for treatment of hRSV infection in monotherapy or in combination with other antivirals.
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Affiliation(s)
- Fryad Rahman
- Department of Biology, College of Science, University of Sulaimani, Kurdistan Region, Iraq.,Department of Molecular Biology, High Quality Laboratory, Anwar Sheikha Medical City, Sulaymaniyah, Iraq
| | - Camille Libre
- Cancer Research Center of Lyon, INSERM U1052 UMR CNRS 5286, Equipe labellisée Ligue Contre le Cancer, Université de Lyon, 69008 Lyon, France
| | - Andrew Oleinikov
- Charles E. Schmidt College of Medicine, Department of Biomedical Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
| | - Sergey Tcherniuk
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris SaclayJouy-en-Josas, France.,Department of Biological Sciences, Youth Academy of Sciences, Kiev, Ukraine
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Evolutionary analysis of human respiratory syncytial virus collected in Myanmar between 2015 and 2018. INFECTION GENETICS AND EVOLUTION 2021; 93:104927. [PMID: 34020068 DOI: 10.1016/j.meegid.2021.104927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/24/2022]
Abstract
We studied genetic variation in the second hypervariable region (HVR) of the G gene of human respiratory syncytial virus (HRSV) from 1701 nasal swab samples collected from outpatients with acute respiratory infections at two general hospitals in the cities Yangon and Pyinmana in Myanmar from 2015 to 2018. HRSV genotypes were characterized using phylogenetic trees constructed using the maximum likelihood method. Time-scale phylogenetic tree analyses were performed using the Bayesian Markov chain Monte Carlo method. In total, 244 (14.3%) samples were HRSV-positive and were classified as HRSV-A (n = 84, 34.4%), HRSV-B (n = 158, 64.8%), and co-detection of HRSV-A/HRSV-B (n = 2, 0.8%). HRSV epidemics occurred seasonally between July (1.9%, 15/785) and August (10.5%, 108/1028), with peak infections in September (35.8%, 149/416) and October (58.2%, 89/153). HRSV infection rate was higher in children ≥1 year of age than in those <1 year of age (70.5% vs. 29.5%). The most common HRSV symptoms in children were cough (80%-90%) and rhinorrhea (70%-100%). The predominant genotypes were ON1for HRSV-A (78%) and BA9 for HRSV-B (64%). Time to the most recent common ancestor was 2014 (95% highest posterior density [HPD], 2012-2015) for HRSV-A ON1 and 2009 (95% HPD, 2004-2012) for HRSV-B BA9. The mean evolutionary rate (substitutions/site/year) for HRSV-B (2.12 × 10-2, 95% HPD, 8.53 × 10-3-3.63 × 10-2) was slightly higher than that for HRSV-A (1.39 × 10-2, 95% HPD, 6.03 × 10-3-2.12 × 10-2). The estimated effective population size (diversity) for HRSV-A increased from 2015 to 2016 and declined in mid-2018, whereas HRSV-B diversity was constant in 2015 and 2016 and increased in mid-2017. In conclusion, the dominant HRSV-A and HRSV-B genotypes in Myanmar were ON1 and BA9, respectively, between 2015 and 2018. HRSV-B evolved slightly faster than HRSV-A and exhibited unique phylogenetic characteristics.
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O'Brien B, Goodridge L, Ronholm J, Nasheri N. Exploring the potential of foodborne transmission of respiratory viruses. Food Microbiol 2021; 95:103709. [PMID: 33397626 PMCID: PMC8035669 DOI: 10.1016/j.fm.2020.103709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 02/07/2023]
Abstract
The ongoing pandemic involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised the question whether this virus, which is known to be spread primarily though respiratory droplets, could be spread through the fecal-oral route or via contaminated food. In this article, we present a critical review of the literature exploring the potential foodborne transmission of several respiratory viruses including human coronaviruses, avian influenza virus (AVI), parainfluenza viruses, human respiratory syncytial virus, adenoviruses, rhinoviruses, and Nipah virus. Multiple lines of evidence, including documented expression of receptor proteins on gastrointestinal epithelial cells, in vivo viral replication in gastrointestinal epithelial cell lines, extended fecal shedding of respiratory viruses, and the ability to remain infectious in food environments for extended periods of time raises the theoretical ability of some human respiratory viruses, particularly human coronaviruses and AVI, to spread via food. However, to date, neither epidemiological data nor case reports of clear foodborne transmission of either viruses exist. Thus, foodborne transmission of human respiratory viruses remains only a theoretical possibility.
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Affiliation(s)
- Bridget O'Brien
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Ste Anne de Bellevue, Québec, Canada
| | | | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Ste Anne de Bellevue, Québec, Canada
| | - Neda Nasheri
- Food Virology Laboratory, Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, ON, Canada.
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Identification of pathogenic genes and transcription factors in respiratory syncytial virus. BMC Pediatr 2021; 21:27. [PMID: 33419394 PMCID: PMC7796524 DOI: 10.1186/s12887-020-02480-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a major cause of acute lower respiratory infections in children, especially bronchiolitis. Our study aimed to identify the key genes and upstream transcription factors in RSV. METHODS To screen for RSV pathogenic genes, an integrated analysis was performed using the RSV microarray dataset in GEO. Functional annotation and potential pathways for differentially expressed genes (DEGs) were further explored by GO and KEGG enrichment analysis. We constructed the RSV-specific transcriptional regulatory network to identify key transcription factors for DEGs in RSV. RESULTS From three GEO datasets, we identified 1059 DEGs (493 up-regulated and 566 down-regulated genes, FDR < 0.05 and |Combined.ES| > 0.8) between RSV patients and normal controls. GO and KEGG analysis revealed that 'response to virus' (FDR = 7.13E-15), 'mitochondrion' (FDR = 1.39E-14) and 'Asthma' (FDR = 1.28E-06) were significantly enriched pathways for DEGs. The expression of IFI27, IFI44, IFITM3, FCER1A, and ISG15 were shown to be involved in the pathogenesis of RSV. CONCLUSIONS We concluded that IFI27, IFI44, IFITM3, FCER1A, and ISG15 may play a role in RSV. Our finding may contribute to the development of new potential biomarkers, reveal the underlying pathogenesis and also identify novel therapeutic targets for RSV.
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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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Rowell CER, Dobrovolny HM. Energy Requirements for Loss of Viral Infectivity. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:281-294. [PMID: 32757142 PMCID: PMC7405386 DOI: 10.1007/s12560-020-09439-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Outside the host, viruses will eventually lose their ability to infect cells due to conformational changes that occur to proteins on the viral capsid. In order to undergo a conformational change, these proteins require energy to activate the chemical reaction that leads to the conformational change. In this study, data from the literature is used to calculate the energy required for viral inactivation for a variety of different viruses by means of the Arrhenius equation. We find that some viruses (rhinovirus, poliovirus, human immunodeficiency virus, Alkhumra hemorrhagic fever virus, and hepatitis A virus) have high inactivation energies, indicative of breaking of a chemical double bond. We also find that several viruses (respiratory syncytial virus, poliovirus, and norovirus) have nonlinear Arrhenius plots, suggesting that there is more than a single pathway for inactivation of these viruses.
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Affiliation(s)
- Caroline E R Rowell
- Department of Chemistry, Wingate University, Hendersonville, NC, USA
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, USA
| | - Hana M Dobrovolny
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, USA.
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14
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Jerbi A, Fodha I, Ben Hamida-Rebai M, Ben Hadj Fredj M, Ataoui I, Bennour H, Abroug S, Khlifa M, Mathlouthi J, Mahdhaoui N, Boussetta K, Trabelsi A. Molecular characterization of respiratory syncytial virus circulating in Tunisia between 2015 and 2018. J Med Microbiol 2020; 69:1203-1212. [PMID: 32755531 DOI: 10.1099/jmm.0.001240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Respiratory syncytial virus (RSV) is the most frequently identified viral agent in children with lower respiratory tract infection (LRTI). No data are available to date regarding RSV genotypes circulating in Tunisia.Aim. The aim of the present study was to investigate the genetic variability of the glycoprotein G gene in Tunisian RSV strains.Methodology. Nasopharyngeal aspirates were collected from infants hospitalized for LRTI in five Tunisian hospitals. All specimens were screened for RSV by a direct immunofluorescence assay (DIFA). To molecularly characterize Tunisian RSV strains, a phylogenetic analysis was conducted. Randomly selected positive samples were subjected to reverse transcription PCR amplifying the second hyper-variable region (HVR2) of the G gene.Results. Among a total of 1417 samples collected between 2015 and 2018, 394 (27.8 %) were positive for RSV by DIFA. Analysis of 61 randomly selected RSV strains revealed that group A RSV (78.7 %) predominated during the period of study as compared to group B RSV (21.3 %). The phylogenetic analysis showed that two genotypes of RSV-A were co-circulating: the ON1 genotype with a 72-nt duplication in HVR2 of the G gene was predominant (98.0 % of RSV-A strains), while one RSV-A strain clustered with the NA1 genotype (2.0 %). Concerning Tunisian group B RSV strains, all sequences contained a 60-nt insertion in HVR2 and a clustered BA10 genotype.Conclusion. These data suggest that RSV-A genotype ON1 and RSV-B genotype BA10, both with duplications in the G gene, were widely circulating in the Central coastal region of Tunisia between 2015 and 2018.
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Affiliation(s)
- Amira Jerbi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Imene Fodha
- Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Meriam Ben Hamida-Rebai
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Mouna Ben Hadj Fredj
- Faculty of Sciences and Techniques, University of Kairouan, Kairouan, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Imene Ataoui
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Haifa Bennour
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Saoussen Abroug
- Pediatric Unit, Sahloul University Hospital, Sousse, Tunisia
| | - Monia Khlifa
- Pediatric Unit, Regional Hospital of Msaken, Sousse, Tunisia
| | - Jihen Mathlouthi
- Neonatology Unit, University Hospital Farhat Hached, Sousse, Tunisia
| | - Nabiha Mahdhaoui
- Neonatology Unit, University Hospital Farhat Hached, Sousse, Tunisia
| | - Khedija Boussetta
- Paediatrics B Department, Children's Hospital of Tunis, Tunis, Tunisia
| | - Abdelhalim Trabelsi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
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15
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Schwartz DA, Dhaliwal A. INFECTIONS IN PREGNANCY WITH COVID-19 AND OTHER RESPIRATORY RNA VIRUS DISEASES ARE RARELY, IF EVER, TRANSMITTED TO THE FETUS: EXPERIENCES WITH CORONAVIRUSES, HPIV, hMPV RSV, AND INFLUENZA. Arch Pathol Lab Med 2020; 144:920-928. [PMID: 32338533 DOI: 10.5858/arpa.2020-0211-sa] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
SARS-CoV-2, the agent of COVID-19, is similar to two other coronaviruses, SARS-CoV and MERS-CoV, in causing life-threatening maternal respiratory infections and systemic complications. Because of global concern for potential intrauterine transmission of SARS-CoV-2 from pregnant women to their infants, this report analyzes the effects on pregnancy of infections caused by SARS-CoV-2 and other respiratory RNA viruses, and examines the frequency of maternal-fetal transmission with SARS-CoV-2, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), influenza, respiratory syncytial virus (RSV), parainfluenza (HPIV) and metapneumovirus (hMPV). There have been no confirmed cases of intrauterine transmission reported with COVID-19 or any other coronavirus infections. Influenza virus, despite causing approximately one billion annual infections globally, has only a few cases of confirmed or suspected intrauterine fetal infections reported. RSV is in an unusual cause of illness among pregnant women, and with the exception of one premature infant with congenital pneumonia, no other cases of maternal-fetal infection are described. Parainfluenza virus and human metapneumovirus can produce symptomatic maternal infections but do not cause intrauterine fetal infection. In summary, it appears that the absence thus far of maternal-fetal transmission of the SARS-CoV-2 virus during the COVID-19 pandemic is similar to other coronaviruses, and is also consistent with the extreme rarity of suggested or confirmed cases of intrauterine transmission of other respiratory RNA viruses. This observation has important consequences for pregnant women as it appears that if intrauterine transmission of SARSCoV-2 does eventually occur, it will be a rare event. Potential mechanisms of fetal protection from maternal viral infections are also discussed.
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Affiliation(s)
- David A Schwartz
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA (Dr. Schwartz); Amareen Dhaliwal, BS, Boston University School of Medicine, Boston, MA, USA (Ms. Dhaliwal)
| | - Amareen Dhaliwal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA (Dr. Schwartz); Amareen Dhaliwal, BS, Boston University School of Medicine, Boston, MA, USA (Ms. Dhaliwal)
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16
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Yun KW, Choi EH, Lee HJ. Molecular epidemiology of respiratory syncytial virus for 28 consecutive seasons (1990-2018) and genetic variability of the duplication region in the G gene of genotypes ON1 and BA in South Korea. Arch Virol 2020; 165:1069-1077. [PMID: 32144544 DOI: 10.1007/s00705-020-04580-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/04/2020] [Indexed: 02/07/2023]
Abstract
We investigated the molecular epidemiology of respiratory syncytial virus (RSV) isolated from children during 28 consecutive seasons (1990-2018) and the genetic variability of the duplication region of RSV genotypes ON1 and BA in South Korea. RSV was identified using culture-based methods in Hep-2 cells and was grouped as RSV-A or RSV-B by an immunofluorescence assay. The second hypervariable region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the duplication region of RSV ON1 and BA were analyzed. A total of 670 RSV-A and 233 RSV-B isolates were obtained. For RSV-A, the NA1 genotype predominated during the 2004/2005-2011/2012 seasons. The ON1 genotype was first detected in 2011 and has since replaced all other genotypes. For RSV-B, the GB3 genotype predominated during the 1999/2000-2005/2006 seasons, but the BA genotype also replaced all other genotypes of RSV-B after the first season in which it was isolated (2005/2006). In ON1 and BA genotype RSV strains, novel sequence types of the duplication region of the G gene were identified in 50-95% and 33-80% of the isolates, respectively, in each season. The ON1 and BA9 genotypes are responsible for the current epidemics of RSV infection in South Korea. The sequences in the duplication region of the G gene have evolved continuously and might be sufficient for the identification of specific strains of the RSV-A ON1 and RSV-B BA genotypes.
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Affiliation(s)
- Ki Wook Yun
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, 03080, South Korea
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, 03080, South Korea
| | - Hoan Jong Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, 03080, South Korea.
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17
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Al-Hassinah S, Parveen S, Somily AM, AlSaadi MM, Alamery SF, Haq SH, Alsenaidy HA, Ahmed A. Evolutionary analysis of the ON1 genotype of subtype a respiratory syncytial virus in Riyadh during 2008-16. INFECTION GENETICS AND EVOLUTION 2019; 79:104153. [PMID: 31881360 DOI: 10.1016/j.meegid.2019.104153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/05/2019] [Accepted: 12/20/2019] [Indexed: 01/07/2023]
Abstract
Respiratory syncytial virus is a leading cause of acute respiratory tract infection (ARI) in children worldwide. Limited information is available on molecular epidemiology of respiratory syncytial virus (RSV) from Saudi Arabia. An attempt was made to identify and characterize RSV strains in nasopharyngeal aspirates collected from hospitalized symptomatic ARI pediatric patients with <5 years of age from Riyadh, Saudi Arabia during 2016. All the samples (n = 100) were tested for RSV by real time PCR. The RSV strains were characterized by sequencing of the second hypervariable region of G protein gene. The study sequences along with the previously reported strains from Saudi Arabia were assessed for mutational, glycosylation, phylogenetic, selection pressure and entropy analyses. Fifty percent of the nasopharyngeal aspirates were positive for RSV. The RSVA (72%) predominated as compared to RSVB (24%) during the study. The study RSVA strains (n = 29) clustered into NA1 and ON1 genotypes whereas all the RSVB sequences (n = 5) were in BA genotype by phylogenetic analysis. Interestingly, 97% of RSVA sequences (n =28) clustered into ON1 genotype with 72 bp duplication in the G protein gene. Numerous mutations, variable N-/O-glycosylation sites and purifying selections were observed in the ON1 genotype. Positive selection with high entropy value was observed for three codons in ON1 (247, 262 and 274 amino acids) indicating higher probability of variations at these positions. Our study shows the progressive emergence and predominance of the ON1 genotype in Riyadh, Saudi Arabia during 2008-16. ON1 genotype almost replaced the previously circulating RSVA strains in this region during this period. Contribution of host genetic and immune factors towards disease severity of the ON1 genotype needs to be investigated in future studies. RSV surveillance in future elaborate investigations are needed in this region to understand its disease burden, evolutionary trajectory and circulation dynamics warranting steps towards vaccine development.
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Affiliation(s)
- Sarah Al-Hassinah
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ali M Somily
- Department of Microbiology, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Muslim Mohammed AlSaadi
- Department of Pediatrics, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Salman Fareeh Alamery
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Centre of Excellence in Biotechnology Research, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Samina Haider Haq
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Anwar Ahmed
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Centre of Excellence in Biotechnology Research, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
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18
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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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19
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Liang X, Liu DH, Chen D, Guo L, Yang H, Shi YS, Wang YJ, Wang WK, Xie ZP, Gao HC, Duan ZJ, Zhang RF. Gradual replacement of all previously circulating respiratory syncytial virus A strain with the novel ON1 genotype in Lanzhou from 2010 to 2017. Medicine (Baltimore) 2019; 98:e15542. [PMID: 31083208 PMCID: PMC6531141 DOI: 10.1097/md.0000000000015542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
ON1 is a novel genotype of human respiratory syncytial virus (HRSV) subtype A, in children with acute respiratory tract infections (ARTIs). However, there is not much data on the prevalence and clinical and molecular characterization in China.Our study is based on the children who had respiratory infections positive for RSV-A admitted by Gansu Provincial Maternity and Child-care Hospital in Lanzhou (northwestern China) during the last 7 epidemic seasons from 2010 to 2017.In our study, different strains of the novel RSV-A genotype ON1, first identified in Canada in December 2010, were first detected in Gansu Provincial Maternity and Child-care Hospital in August 2012 and then followed by an abrupt expansion in the number of ON1 variants in the beginning of 2014 and eventually replaced all other RSV-A strains from 2015 to 2017. ON1 is characterized by a 72-nt duplication in the C-terminal region of the highly variable attachment glycoprotein (G), predicted to lengthen the polypeptide with 24 amino acids, including a 23-aa duplication, which likely changes antigenicity. New N-glycosylation sites occurred within the 23-aa duplication and 24-aa insertion of the ON1 viruses in our study. Notably, RSV infections occurred later, but peaked sooner from the 2014/2015 to 2016/2017 epidemic seasons, compared with the previous 4 seasons.Our study concluded that genotype ON1 has caused larger outbreaks and became the predominate genotype for HRSV subgroup A in Lanzhou from 2013 to 2017, and became the sole genotype of RSV-A in 2015/2016 and 2016/2017. Our data indicate that northwest of China and the world will eventually be dominated by the ON1 RSV-A genotype, including the possibility for vaccine development. Based on trends seen in RSV-B BA genotype, which predominated for decades, there is a possibility to develop a vaccine for children in the next 10 years.
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Affiliation(s)
- Xuan Liang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
- Gansu University of Chinese Medicine, Lanzhou
| | - Dong-Hai Liu
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
- Gansu University of Chinese Medicine, Lanzhou
| | - De Chen
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Li Guo
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Hui Yang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Yong-Sheng Shi
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Yong-Jun Wang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Wei-Kai Wang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Zhi-Ping Xie
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Han-Chun Gao
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhao-Jun Duan
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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20
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Vos LM, Oosterheert JJ, Kuil SD, Viveen M, Bont LJ, Hoepelman AIM, Coenjaerts FEJ. High epidemic burden of RSV disease coinciding with genetic alterations causing amino acid substitutions in the RSV G-protein during the 2016/2017 season in The Netherlands. J Clin Virol 2019; 112:20-26. [PMID: 30708281 DOI: 10.1016/j.jcv.2019.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/11/2019] [Accepted: 01/20/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND We found amino acid substitutions in the Gglycoprotein of respiratory syncytial virus (RSV) A during the 2016/2017 epidemic in The Netherlands. OBJECTIVES We evaluated whether these alterations led to increased RSV incidence and disease burden. STUDY DESIGN We sequenced the gene encoding the G-protein of prospectively collected clinical specimens from secondary care adult patients testing positive for RSV during the 2016/2017 and 2017/2018 epidemic RSV season. We evaluated associations between genetic, clinical and epidemiological data. RESULTS We included 49 RSV strains. In 2016/2017 28 strains were included, 20 community acquired RSV-A, 5 hospital acquired RSV-A and 3 community acquired RSV-B. In 2017/2018 21 strains were included, 8 community acquired RSV-A and 13 community acquired RSV-B. G-proteins of 10 out of the 20 community acquired 2016/2017 RSV-A strains shared a set of eight novel amino acid substitutions of which seven in mucin-like regions 1 and 2 and one in the heparin binding domain. This genetic variant was no longer detected among 2017/2018 RSV-A strains. Among patients carrying the novel RSV-A strain-type, 30% died. CONCLUSIONS A set of eight amino acid substitutions was found in 50% of the 2016/2017 community acquired RSV-A G-proteins. This combination of substitutions was globally never observed before. The appearance of this new strain-type coincided with an increased RSV peak in The Netherlands and was associated with higher disease severity. The transient character of this epidemic strain-type suggests rapid clearance of this lineage in our study community.
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Affiliation(s)
- Laura M Vos
- University Medical Center Utrecht, Utrecht University, Department of Internal Medicine and Infectious Diseases, Utrecht 3584 CX, The Netherlands.
| | - Jan Jelrik Oosterheert
- University Medical Center Utrecht, Utrecht University, Department of Internal Medicine and Infectious Diseases, Utrecht 3584 CX, The Netherlands
| | - Sacha D Kuil
- Academic Medical Center Amsterdam, Department of Medical Microbiology, Laboratory of Clinical Virology, Amsterdam 1105 AZ, The Netherlands
| | - Marco Viveen
- University Medical Center Utrecht, Utrecht University, Department of Medical Microbiology, Utrecht 3584 CX, The Netherlands
| | - Louis J Bont
- Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Department of Pediatric Infectious Diseases, Utrecht 3584 EA, The Netherlands
| | - Andy I M Hoepelman
- University Medical Center Utrecht, Utrecht University, Department of Internal Medicine and Infectious Diseases, Utrecht 3584 CX, The Netherlands
| | - Frank E J Coenjaerts
- University Medical Center Utrecht, Utrecht University, Department of Medical Microbiology, Utrecht 3584 CX, The Netherlands
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21
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González-Parra G, Dobrovolny HM. A quantitative assessment of dynamical differences of RSV infections in vitro and in vivo. Virology 2018; 523:129-139. [PMID: 30144786 DOI: 10.1016/j.virol.2018.07.027] [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: 04/22/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 10/28/2022]
Abstract
Experimental results in vitro and in animal models are used to guide researchers in testing vaccines or treatment in humans. However, viral kinetics are different in vitro, in animals, and in humans, so it is sometimes difficult to translate results from one system to another. In this study, we use a mathematical model to fit experimental data from multiple cycle respiratory syncytial virus (RSV) infections in vitro, in african green monkey (AGM), and in humans in order to quantitatively compare viral kinetics in the different systems. We find that there are differences in viral clearance rate, productively infectious cell lifespan, and eclipse phase duration between in vitro and in vivo systems and among different in vivo systems. We show that these differences in viral kinetics lead to different estimates of drug effectiveness of fusion inhibitors in vitro and in AGM than in humans.
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Affiliation(s)
| | - Hana M Dobrovolny
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, United States.
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22
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Madi N, Chehadeh W, Asadzadeh M, Al-Turab M, Al-Adwani A. Analysis of genetic variability of respiratory syncytial virus groups A and B in Kuwait. Arch Virol 2018; 163:2405-2413. [PMID: 29777370 PMCID: PMC7087269 DOI: 10.1007/s00705-018-3881-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/07/2018] [Indexed: 01/22/2023]
Abstract
Respiratory syncytial virus (RSV) is the most frequently identified viral agent in infants, children, and elderly people with acute respiratory tract infections (ARTIs). This study is the only one of its kind in Kuwait, and its purpose was to investigate the genetic variability of the G protein gene in RSV strains prevalent in Kuwait. Respiratory samples were collected from patients with ARTIs in various hospitals in Kuwait and subjected to reverse transcription PCR (RT-PCR) amplifying a fragment of the G gene of RSV. A total of 305 samples were collected between January and mid-December 2016, and 77 (25.2%) were positive for RSV. Group A viruses were predominant over group B viruses; the RSV-A group was detected in 52 (67.5%) of the positive samples, while the RSV-B group was detected in 25 (32.5%) of the positive samples. Phylogenetic analysis showed that all RSV-A strains grouped into eight clusters of identical sequences of untyped strains. Twelve RSV-B strains, on the other hand, belonged to the RSV-B/BA10 genotype, while the rest were untyped. These data suggest that new and untyped strains of RSV-A group likely predominated in Kuwait and that the BA10 genotype of the RSV-B group became the dominant genotype in the 2016 season.
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Affiliation(s)
- Nada Madi
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait.
| | - Wassim Chehadeh
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
| | - Mohammed Asadzadeh
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
| | - Mariam Al-Turab
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
| | - Anfal Al-Adwani
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
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Hibino A, Saito R, Taniguchi K, Zaraket H, Shobugawa Y, Matsui T, Suzuki H. Molecular epidemiology of human respiratory syncytial virus among children in Japan during three seasons and hospitalization risk of genotype ON1. PLoS One 2018; 13:e0192085. [PMID: 29377949 PMCID: PMC5788364 DOI: 10.1371/journal.pone.0192085] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/16/2018] [Indexed: 12/25/2022] Open
Abstract
We investigated the genetic diversity, the circulation patterns, and risk for hospital admission of human respiratory syncytial virus (HRSV) strains in Japan between 2012 through 2015. During the study period, 744 HRSV-positive cases were identified by rapid diagnostic test. Of these, 572 samples were positive by real-time PCR; 400 (69.9%) were HRSV-A, and 172 (30.1%) were HRSV-B. HRSV-A and -B alternated as the dominant strain in the subsequent seasons. Phylogenetic tree analysis of the second hyper-variable region of the G protein classified the HRSV-A specimens into NA1 (n = 242) and ON1 (n = 114) genotypes and the HRSV-B specimens into BA9 (n = 60), and BA10 (n = 27). The ON1 genotype, containing a 72-nucleotide duplication in the G protein’s second hyper-variable region, was first detected in the 2012–2013 season but it predominated and replaced the older NA1 HRSV-A in the 2014–2015 season, which also coincided with a record number of HRSV cases reported to the National Infectious Disease Surveillance in Japan. The risk of hospitalization was 6.9 times higher for the ON1 genotype compared to NA1. In conclusion, our data showed that the emergence and predominance of the relatively new ON1 genotype in Japan was associated with a record high number of cases and increased risk for hospitalization.
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Affiliation(s)
- Akinobu Hibino
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- * E-mail:
| | | | - Hassan Zaraket
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Pathology, Immunology, and Microbiology, Faculty of Medicine American University of Beirut, Beirut, Lebanon
- Center for Infectious Disease Research, Faculty of Medicine American University of Beirut, Beirut, Lebanon
| | - Yugo Shobugawa
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tamano Matsui
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Suzuki
- School of Nursing, Niigata Seiryo University, Niigata, Japan
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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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Molecular and clinical characterization of human respiratory syncytial virus in South Korea between 2009 and 2014. Epidemiol Infect 2017; 145:3226-3242. [PMID: 28988544 DOI: 10.1017/s0950268817002230] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Respiratory syncytial virus (RSV) can cause serious respiratory infections, second only to influenza virus. In order to know RSV's genetic changes we examined 4028 respiratory specimens from local hospital outpatients in Gyeonggi Province, South Korea over six consecutive years by real-time one-step RT-PCR; 183 patients were positive for RSV infection. To investigate the specific distribution of RSV genotypes, we performed partial sequencing of the glycoprotein gene. Of the 131 RSV-A specimens sequenced, 61 (43·3%) belonged to the ON1 genotype, 66 (46·8%) were NA1 genotype, 3 (2·1%) were GA5 genotype, and 1 (0·7%) belonged to the GA1 genotype. Of the 31 RSV-B specimens sequenced, 29 were BA9 genotype (87·9%) and 2 were BA10 genotype (6·1%). The most common clinical symptoms were fever, cough, nasal discharge, and phlegm; multiple logistic regression analysis showed that RSV-positive infection on pediatric patients was strongly associated with cough (OR = 2·8, 95% CI 1·6-5·1) and wheezing (OR = 2·8, 95% CI 1·7-4·4). The ON1 genotype was significantly associated with phlegm (OR = 11·8, 95% CI 3·8-46·7), while the NA1 genotype was associated with the pediatric patients' gender (males, OR = 2·4, 95% CI 1·1-5·4) and presence of chills (OR = 5·1, 95% CI 1·1-27·2). RSV subgroup B was showed association with nasal obstruction (OR = 4·6, 95% CI 1·2-20·0). The majority of respiratory virus coinfections with RSV were human rhinovirus (47·2%). This study contributes to our understanding of the molecular epidemiological characteristics of RSV, which promotes the potential for improving RSV vaccines.
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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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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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Yoshihara K, Le MN, Nagasawa K, Tsukagoshi H, Nguyen HA, Toizumi M, Moriuchi H, Hashizume M, Ariyoshi K, Dang DA, Kimura H, Yoshida LM. Molecular evolution of respiratory syncytial virus subgroup A genotype NA1 and ON1 attachment glycoprotein (G) gene in central Vietnam. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 45:437-446. [PMID: 27746294 DOI: 10.1016/j.meegid.2016.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 01/08/2023]
Abstract
We performed molecular evolutionary analyses of the G gene C-terminal 3rd hypervariable region of RSV-A genotypes NA1 and ON1 strains from the paediatric acute respiratory infection patients in central Vietnam during the 2010-2012 study period. Time-scaled phylogenetic analyses were performed using Bayesian Markov Chain Monte Carlo (MCMC) method, and pairwise distances (p-distances) were calculated. Bayesian Skyline Plot (BSP) was constructed to analyze the time-trend relative genetic diversity of central Vietnam RSV-A strains. We also estimated the N-glycosylation sites within G gene hypervariable region. Amino acid substitutions under positive and negative selection pressure were examined using Conservative Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), Internal Fixed Effects Likelihood (IFEL) and Mixed Effects Model for Episodic Diversifying Selection (MEME) models. The majority of central Vietnam ON1 strains detected in 2012 were classified into lineage 1 with few positively selected substitutions. As for the Vietnamese NA1 strains, four lineages were circulating during the study period with a few positive selection sites. Shifting patterns of the predominantly circulating NA1 lineage were observed in each year during the investigation period. Median p-distance of central Vietnam NA1 strains was wider (p-distance=0.028) than that of ON1 (p-distance=0.012). The molecular evolutionary rate of central Vietnam ON1 strains was estimated to be 2.55×10-2 (substitutions/site/year) and was faster than NA1 (7.12×10-3 (substitutions/site/year)). Interestingly, the evolutionary rates of both genotypes ON1 and NA1 strains from central Vietnam were faster than the global strains respectively. Furthermore, the shifts of N-glycosylation pattern within the G gene 3rd hypervariable region of Vietnamese NA1 strains were observed in each year. BSP analysis indicated the rapid growth of RSV-A effective population size in early 2012. These results suggested that the molecular evolution of RSV-A G gene detected in central Vietnam was fast with unique evolutionary dynamics.
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Affiliation(s)
- Keisuke Yoshihara
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Minh Nhat Le
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Gunma 371-0052, Japan
| | - Hien Anh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Michiko Toizumi
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Hiroyuki Moriuchi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan; Department of Paediatrics, Nagasaki University Hospital, Nagasaki 852-8102, Japan
| | - Masahiro Hashizume
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Koya Ariyoshi
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
| | - Lay-Myint Yoshida
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan.
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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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Fan R, Fan C, Zhang J, Wen B, Lei Y, Liu C, Chen L, Liu W, Wang C, Qu X. Respiratory syncytial virus subtype ON1/NA1/BA9 predominates in hospitalized children with lower respiratory tract infections. J Med Virol 2016; 89:213-221. [PMID: 27358012 PMCID: PMC7166484 DOI: 10.1002/jmv.24619] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 12/02/2022]
Abstract
Respiratory syncytial virus (RSV) infection is the leading cause of acute respiratory tract disease in children less than 5 years old. The aim of this study was to further elucidate the molecular properties and clinical characteristics of RSV infection. The study sample included 238 patients <5 years old who were hospitalized with clinical symptoms of upper or lower respiratory tract infection (URTI or LRTI) in the Pediatric Department at the First People's Hospital of Chenzhou, South China in 2014. We subjected nasopharyngeal aspirate (NPA) or nasal swab (NS) samples from the patients to indirect fluorescence assay screens. RSV G genes were amplified by reverse transcription‐PCR (RT‐PCR) and sequenced. Of the 238 patients screened, 64 (26.8%) were confirmed to have RSV infections. Of those 64 confirmed RSV infection cases, 39 (60.9%) had subtype BA9, 13 (20.3%) had the recently identified subtype ON1, 11 (17.2%) had subtype NA1, and 1 (1.6%) had subtype GB2. The predominant presentation was LRTI with coughing, sputum production, fever, and wheezing. RSV subtype NA1 and BA9 infections were found mostly in infants, whereas the age distribution of subtype ON1 infections was more uniform across the age bands. Phylogenetic analysis indicated that, compared with the prototype strain A2, all ON1 and most NA1 isolates had lost one potential N‐glycosylation site at amino acid 251 and 249 due to T251K and N249Y substitution, respectively. These findings suggest that NA1, BA9, and ON1 are the dominant RSV subtypes causing respiratory tract infections in young children presenting to the hospital in South China. J. Med. Virol. 89:213–221, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ruyan Fan
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China.,Department of Pediatric, Guangzhou Women and Children's Medical Center, Guangzhou, People's Republic of China
| | - Chuping Fan
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Jian Zhang
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Bo Wen
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Yefei Lei
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Chan Liu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Lijuan Chen
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Wenpei Liu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Chuan Wang
- Department of Public Health, Sichuan University, Chengdu, People's Republic of China
| | - Xiaowang Qu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
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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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32
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Do LAH, Wilm A, van Doorn HR, Lam HM, Sim S, Sukumaran R, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Dac NAT, Trinh HN, Nguyen TTH, Binh BTL, Le K, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, Farrar J, de Jong M, Chen S, Nagarajan N, Bryant JE, Hibberd ML. Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution. J Gen Virol 2016; 96:3470-3483. [PMID: 26407694 DOI: 10.1099/jgv.0.000298] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children ,2 years of age. Little is known about RSV intra-host genetic diversity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive samples (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our samples, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites inG were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic diversity. We further identified hotspots and coldspots of intra-host genetic diversity in the RSV genome, some of which may highlight previously unknown regions of functional importance.
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Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Andreas Wilm
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ha Minh Lam
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Shuzhen Sim
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - Rashmi Sukumaran
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - Anh Tuan Tran
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Bach Hue Nguyen
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thi Thu Loan Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quynh Huong Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quoc Bao Vo
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | | | - Hong Nhien Trinh
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | | | - Bao Tinh Le Binh
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Khanh Le
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Minh Tien Nguyen
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Quang Tung Thai
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thanh Vu Vo
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | | | - Thi Kim Huyen Dang
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Ngoc Huong Cao
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Thu Van Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Lu Viet Ho
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Menno de Jong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Swaine Chen
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | | | - Juliet E Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Martin L Hibberd
- Genome Institute of Singapore, Genome Building, 138672 Singapore
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Association of RSV-A ON1 genotype with Increased Pediatric Acute Lower Respiratory Tract Infection in Vietnam. Sci Rep 2016; 6:27856. [PMID: 27306333 PMCID: PMC4910061 DOI: 10.1038/srep27856] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/26/2016] [Indexed: 12/26/2022] Open
Abstract
Since the initial discovery of RSV-A ON1 in Canada in 2010, ON1 has been reported worldwide, yet information regarding its clinical impact and severity has been controversial. To investigate the clinical relevance of RSV-A ON1,acute respiratory infection (ARI) cases enrolled to our population-based prospective pediatric ARI surveillance at Khanh Hoa General Hospital, Central Vietnam from January 2010 through December 2012 were studied. Clinical-epidemiological information and nasopharyngeal samples were collected. Multiplex PCR assays were performed for screening 13 respiratory viruses. RSV-positive samples were further tested for subgroups (A/B) and genotypes information by sequencing the G-glycoprotein 2nd hypervariable region. Statistical analysis was performed to evaluate the clinical-epidemiological characteristics of RSV-A ON1. A total of 1854 ARI cases were enrolled and 426 (23.0%) of them were RSV-positive. During the study period, RSV-A and B had been co-circulating. NA1 was the predominant RSV-A genotype until the appearance of ON1 in 2012. RSV-related ARI hospitalization incidence significantly increased after the emergence of ON1. Moreover, multivariate analysis revealed that risk of lower respiratory tract infection was 2.26 (95% CI: 1.37-3.72) times, and radiologically-confirmed pneumonia was 1.98 (95% CI: 1.01-3.87) times greater in ON1 compared to NA1 cases. Our result suggested that ON1 ARI cases were clinically more severe than NA1.
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Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene. Sci Rep 2016; 6:26311. [PMID: 27212633 PMCID: PMC4876326 DOI: 10.1038/srep26311] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 05/03/2016] [Indexed: 11/25/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) is responsible for considerable morbidity and mortality worldwide and is the most important respiratory viral pathogen in infants. Extensive sequence variability within and between RSV group A and B viruses and the ability of multiple clades and sub-clades of RSV to co-circulate are likely mechanisms contributing to the evasion of herd immunity. Surveillance and large-scale whole-genome sequencing of RSV is currently limited but would help identify its evolutionary dynamics and sites of selective immune evasion. In this study, we performed complete-genome next-generation sequencing of 92 RSV isolates from infants in central Tennessee during the 2012–2014 RSV seasons. We identified multiple co-circulating clades of RSV from both the A and B groups. Each clade is defined by signature N- and O-linked glycosylation patterns. Analyses of specific RSV genes revealed high rates of positive selection in the attachment (G) gene. We identified RSV-A viruses in circulation with and without a recently reported 72-nucleotide G gene sequence duplication. Furthermore, we show evidence of convergent evolution of G gene sequence duplication and fixation over time, which suggests a potential fitness advantage of RSV with the G sequence duplication.
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Malasao R, Okamoto M, Chaimongkol N, Imamura T, Tohma K, Dapat I, Dapat C, Suzuki A, Saito M, Saito M, Tamaki R, Pedrera-Rico GAG, Aniceto R, Quicho RFN, Segubre-Mercado E, Lupisan S, Oshitani H. Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012-2013. PLoS One 2015; 10:e0142192. [PMID: 26540236 PMCID: PMC4635013 DOI: 10.1371/journal.pone.0142192] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/19/2015] [Indexed: 12/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of acute lower respiratory tract infections in infants and children worldwide. We performed molecular analysis of HRSV among infants and children with clinical diagnosis of severe pneumonia in four study sites in the Philippines, including Biliran, Leyte, Palawan, and Metro Manila from June 2012 to July 2013. Nasopharyngeal swabs were collected and screened for HRSV using real-time polymerase chain reaction (PCR). Positive samples were tested by conventional PCR and sequenced for the second hypervariable region (2nd HVR) of the G gene. Among a total of 1,505 samples, 423 samples were positive for HRSV (28.1%), of which 305 (72.1%) and 118 (27.9%) were identified as HRSV-A and HRSV-B, respectively. Two genotypes of HRSV-A, NA1 and ON1, were identified during the study period. The novel ON1 genotype with a 72-nucleotide duplication in 2nd HVR of the G gene increased rapidly and finally became the predominant genotype in 2013 with an evolutionary rate higher than the NA1 genotype. Moreover, in the ON1 genotype, we found positive selection at amino acid position 274 (p<0.05) and massive O- and N-glycosylation in the 2nd HVR of the G gene. Among HRSV-B, BA9 was the predominant genotype circulating in the Philippines. However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains. These findings suggest that HRSV is an important cause of severe acute respiratory infection among children in the Philippines and revealed the emergence and subsequent predominance of the ON1 genotype and the sporadic detection of the GB2 genotype. Both genotypes were detected for the first time in the Philippines.
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Affiliation(s)
| | - Michiko Okamoto
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | | | - Kentaro Tohma
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Isolde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Clyde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Suzuki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayuko Saito
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | - Raita Tamaki
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | | | - Rapunzel Aniceto
- Eastern Visayas Regional Medical Center, Tacloban City, Philippines
| | | | | | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
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36
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Ivancic-Jelecki J, Forcic D, Mlinaric-Galinovic G, Tesovic G, Nikic Hecer A. Early Evolution of Human Respiratory Syncytial Virus ON1 Strains: Analysis of the Diversity in the C-Terminal Hypervariable Region of Glycoprotein Gene within the First 3.5 Years since Their Detection. Intervirology 2015; 58:172-80. [PMID: 26112390 DOI: 10.1159/000382018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/31/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Characterization of the phylogeny and diversity of human respiratory syncytial virus (HRSV) genotype ON1 that occurred during its early evolution (within the first 3.5 years since the detection of the first ON1 strains). ON1 strains have a 72-nucleotide-long in-frame duplication within the second hypervariable domain of the glycoprotein gene (HVR2). METHODS All available HVR2 sequences of strains belonging to the ON1 genotype published prior to June 20, 2014 were collected. Multiple sequence alignments, phylogeny, phylogeography, sequence clustering and putative protein analyses were performed. RESULTS The worldwide spread and diversification of ON1 strains are presented. Only in a minority of ON1 strains do the two replicas remain identical, and various ON1 strains possess common differences between the first and the second copy (segments A and B). Mutations of the progenitor sequence were more frequent in segment B, a higher overall diversity on the protein level and more putative glycosylation sites exist in segment B, and, unlike in segment A, positive selection acts on that protein region. CONCLUSIONS The fast spread of the novel HRSV genotype ON1 has been accompanied by its rapid concurrent diversification. Differences in variability of the two replicas within HVR2 were detected, with C-terminal replica being more variable.
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Affiliation(s)
- Jelena Ivancic-Jelecki
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia
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37
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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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38
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Cui G, Zhu R, Deng J, Zhao L, Sun Y, Wang F, Qian Y. Rapid replacement of prevailing genotype of human respiratory syncytial virus by genotype ON1 in Beijing, 2012-2014. INFECTION GENETICS AND EVOLUTION 2015; 33:163-8. [PMID: 25929164 DOI: 10.1016/j.meegid.2015.04.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/15/2015] [Accepted: 04/26/2015] [Indexed: 11/19/2022]
Abstract
Human respiratory syncytial virus (HRSV) is the most common viral pathogen causing lower respiratory infections in infants and young children worldwide. HRSV ON1 genotype in subgroup A with a characteristic of a 72 nucleotide duplication in the second highly variable region of attachment glycoprotein gene, has been reported in some countries since it was first detected in clinical samples collected in Canada in 2010. In this study, 557 HRSV antigen-positive nasopharyngeal aspirates were randomly selected during 2012/2013 to 2013/2014 HRSV seasons in Beijing for subgroup typing and for ON1 genotype screening by using a PCR based method developed for easily identifying genotype ON1 out of strains of subtype A. It was found that subgroup B was dominant in the 2012/2013 season and sudden shift of subgroup dominance from B to A and rapid replacement of previously prevailing NA1 genotype by ON1 genotype occurred in the 2013/2014 season. Reversible amino acid replacement in the G protein gene was found in a new branch of ON1 genotype. The evolutionary rate of the 351 global ON1 sequences was estimated to 7.34 × 10(-3) nucleotide substitutions per site per year (95% highest probability density intervals, HPD, 5.71 × 10(-3) to 9.04 × 10(-3)), with the time of most recent common ancestor dating back to June 2009.
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Affiliation(s)
- Guanglin Cui
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Runan Zhu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Jie Deng
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Linqing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Yu Sun
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Fang Wang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Yuan Qian
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China.
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Complete genome sequences of human respiratory syncytial virus genotype a and B isolates from South Korea. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00332-15. [PMID: 25908140 PMCID: PMC4408341 DOI: 10.1128/genomea.00332-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
There is a paucity of complete genome sequence information for human respiratory syncytial virus (HRSV). To this end, we sequenced the complete genome sequences of HRSV genotype A (HRSV-A/IC688/12) and genotype B (HRSV-B/GW0047/14 and HRSV-B/IC0027/14). This information will increase the understanding of HRSV genetic diversity, evolution, pathogenicity, antigenicity, and transmissibility.
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40
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Complete genome sequences of one human respiratory syncytial antigenic group a virus from china and its four mouse-adapted isolates. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00062-15. [PMID: 25744999 PMCID: PMC4358386 DOI: 10.1128/genomea.00062-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, one human respiratory syncytial antigenic group A virus (HRSV-A-GZ08-0) and its four BALB/c mouse-adapted isolates were sequenced and elucidated. Nineteen nucleotides were mutated between HRSV-A-GZ08-0 and the four mouse-adapted isolates.
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41
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Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. J Virol 2015; 89:3444-54. [PMID: 25609811 PMCID: PMC4403408 DOI: 10.1128/jvi.03391-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is associated with severe childhood respiratory infections. A clear description of local RSV molecular epidemiology, evolution, and transmission requires detailed sequence data and can inform new strategies for virus control and vaccine development. We have generated 27 complete or nearly complete genomes of RSV from hospitalized children attending a rural coastal district hospital in Kilifi, Kenya, over a 10-year period using a novel full-genome deep-sequencing process. Phylogenetic analysis of the new genomes demonstrated the existence and cocirculation of multiple genotypes in both RSV A and B groups in Kilifi. Comparison of local versus global strains demonstrated that most RSV A variants observed locally in Kilifi were also seen in other parts of the world, while the Kilifi RSV B genomes encoded a high degree of variation that was not observed in other parts of the world. The nucleotide substitution rates for the individual open reading frames (ORFs) were highest in the regions encoding the attachment (G) glycoprotein and the NS2 protein. The analysis of RSV full genomes, compared to subgenomic regions, provided more precise estimates of the RSV sequence changes and revealed important patterns of RSV genomic variation and global movement. The novel sequencing method and the new RSV genomic sequences reported here expand our knowledge base for large-scale RSV epidemiological and transmission studies. IMPORTANCE The new RSV genomic sequences and the novel sequencing method reported here provide important data for understanding RSV transmission and vaccine development. Given the complex interplay between RSV A and RSV B infections, the existence of local RSV B evolution is an important factor in vaccine deployment.
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Agoti CN, Otieno JR, Gitahi CW, Cane PA, Nokes DJ. Rapid spread and diversification of respiratory syncytial virus genotype ON1, Kenya. Emerg Infect Dis 2015; 20:950-9. [PMID: 24856417 PMCID: PMC4036793 DOI: 10.3201/eid2006.131438] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Surveillance of this new genotype helps clarify the mechanisms of rapid emergence of respiratory viruses. Respiratory syncytial virus genotype ON1, which is characterized by a 72-nt duplication in the attachment protein gene, has been detected in >10 countries since first identified in Ontario, Canada, in 2010. We describe 2 waves of genotype ON1 infections among children admitted to a rural hospital in Kenya during 2012. Phylogenetic analysis of attachment protein gene sequences showed multiple introductions of genotype ON1; variants distinct from the original Canadian viruses predominated in both infection waves. The genotype ON1 dominated over the other group A genotypes during the second wave, and some first wave ON1 variants reappeared in the second wave. An analysis of global genotype ON1 sequences determined that this genotype has become considerably diversified and has acquired signature coding mutations within immunogenic regions, and its most recent common ancestor dates to ≈2008–2009. Surveillance of genotype ON1 contributes to an understanding of the mechanisms of rapid emergence of respiratory viruses.
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43
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Avadhanula V, Chemaly RF, Shah DP, Ghantoji SS, Azzi JM, Aideyan LO, Mei M, Piedra PA. Infection with novel respiratory syncytial virus genotype Ontario (ON1) in adult hematopoietic cell transplant recipients, Texas, 2011-2013. J Infect Dis 2014; 211:582-9. [PMID: 25156562 DOI: 10.1093/infdis/jiu473] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) can cause severe respiratory disease in adult hematopoietic cell transplant (HCT) recipients. RSV subgroups A and B have evolved into multiple genotypes. We report on a recently described RSV genotype (ON1) in a cohort of adult HCT recipients in Texas. METHODS Twenty adult HCT recipients were enrolled as a part of an efficacy trial of ribavirin therapy. RSV identification and genotyping was performed using molecular techniques. RSV-specific neutralizing antibody (NAb) responses were measured. RESULTS ON1 genotype was detected in 3 of 6 patients in the 2011-2012 season and in 8 of 14 patients in 2012-2013 season. Other genotypes detected were NA1 and BA. NAb levels were low at enrollment. Eight of 9 patients who cleared the RSV infection within 2 weeks mounted a ≥4-fold NAb response, compared with 2 of 8 who shed the virus for >2 weeks. The clinical course of those infected with ON1 was comparable to the course for individuals infected with other genotypes. CONCLUSION This is the first report of RSV ON1 genotype in the United States, and ON1 genotype was dominant genotype in adult HCT recipients. Interestingly, faster viral clearance was associated with a ≥4-fold NAb response, likely indicating a reconstituted immune system.
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Affiliation(s)
| | - Roy F Chemaly
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dimpy P Shah
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shashank S Ghantoji
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jacques M Azzi
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Minghua Mei
- Department of Molecular Virology and Microbiology
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology Department of Pediatrics, Baylor College of Medicine
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The genetic variability of glycoproteins among respiratory syncytial virus subtype A in China between 2009 and 2013. INFECTION GENETICS AND EVOLUTION 2014; 27:339-47. [PMID: 25109878 DOI: 10.1016/j.meegid.2014.07.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 11/21/2022]
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections in infants and children under 5years of age. The novel genotype ON1 has a 72-nucleotide duplication, which is the largest duplicated genome portion of RSV. Whether the ON1 genotype will follow the pattern of the BA genotype, which has a 60-nucleotide duplication, and become the predominant RSV-A strain is a global concern. To obtain information regarding the prevalence of the ON1 genotype in Chongqing in Southwestern China, we examined the circulation pattern of RSV-A identified over four consecutive years (June 2009 to August 2013). In this study, 312 (12%) RSV-A strains were isolated from 2601 nasopharyngeal aspirates, and partial G gene was sequenced successfully in 250 isolates. Of the sequenced Chongqing RSV-A isolates, 237 (94.8%) strains were the NA1 genotype, 4 (1.6%) strains were the NA3 genotype, 4 (1.6%) strains were the NA4 genotype, 1 (0.4%) strain was the GA1 genotype, and 4 (1.6%) strains were identified as the ON1 genotype. Analysis of the distribution, phylogeny, and evolution of the ON1 strains that were collected globally until December 2013 revealed that the ON1 genotype has rapidly disseminated across the world under positive selection pressures. Future studies will determine whether this new genotype will continue to spread and become the dominant strain of RSV-A worldwide. These findings may contribute to the understanding of RSV evolution and to the potential development of a vaccine against RSV.
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Liu J, Mu Y, Dong W, Yao F, Wang L, Yan H, Lan K, Zhang C. Genetic variation of human respiratory syncytial virus among children with fever and respiratory symptoms in Shanghai, China, from 2009 to 2012. INFECTION GENETICS AND EVOLUTION 2014; 27:131-6. [PMID: 25046173 DOI: 10.1016/j.meegid.2014.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/29/2022]
Abstract
Human respiratory syncytial virus (HRSV) of genus Pneumovirus is one of the most common pathogens causing severe acute lower respiratory tract infection in infants and children. No information on the genotype distribution of HRSV is available in East China (e.g. Shanghai). From August 2009 to December 2012, 2407 nasopharyngeal swabs were collected from outpatient children with fever and respiratory symptoms in Shanghai. HRSV infection was determined using a multiplex RT-PCR assay. The second hypervariable region (HVR2) of G protein gene of HRSV was amplified and sequenced from HRSV positive samples. Genotypes were characterized by phylogenetic analyses. Of 2407 nasopharyngeal samples, 184 (7.6%) were tested as HRSV positive. From 160 positive subjects with sufficient nasopharyngeal samples, 69 HVR2 sequences were obtained by RT-PCR and sequencing. Three HRSV epidemic seasons were observed from August 2009 to December 2012, and an extreme outbreak of HRSV occurred in the 2009-2010 epidemic season. A genotype shift of predominant HRSV strains from B group in the 2009-2010 epidemic season to group A in the subsequent epidemic seasons was observed. Ten HRSV genotypes, including four group A genotypes NA1, NA3, NA4, and ON1, and six group B genotypes BA9, BA10, SAB4, CB1, BAc, and BA?, were detected in Shanghai. Seven genotypes (NA1, BA9-10, SAB4, CB1, BAc and BA?) were found in the 2009-2010 epidemic season. The co-circulation of multiple genotypes was associated with the extreme outbreak of HRSV among children with fever and respiratory symptoms in the 2009-2010 epidemic season.
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Affiliation(s)
- Jia Liu
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai 200025, China
| | - Yonglin Mu
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai 200025, China; College of Life and Environmental Science, Shanghai Normal University, Shanghai 200234, China
| | - Wei Dong
- Pediatric Department, Shanghai Nanxiang Hospital, Jiading District, Shanghai 201800, China
| | - Fujia Yao
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai 200025, China
| | - Lili Wang
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai 200025, China
| | - Huajie Yan
- Pediatric Department, Shanghai Nanxiang Hospital, Jiading District, Shanghai 201800, China
| | - Ke Lan
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai 200025, China.
| | - Chiyu Zhang
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai 200025, China.
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Kim YJ, Kim DW, Lee WJ, Yun MR, Lee HY, Lee HS, Jung HD, Kim K. Rapid replacement of human respiratory syncytial virus A with the ON1 genotype having 72 nucleotide duplication in G gene. INFECTION GENETICS AND EVOLUTION 2014; 26:103-12. [PMID: 24820343 PMCID: PMC7106136 DOI: 10.1016/j.meegid.2014.05.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/23/2014] [Accepted: 05/05/2014] [Indexed: 02/01/2023]
Abstract
We investigated the prevalence of HRSV during 2008–2013. Novel HRSV-A ON1 genotype was emerged in August 2011. After 1 year of emergence in 2012–2013, 94.6% was replaced with novel ON1 genotype. Evolutionary dynamics also drastically increased in 2011. The result of epitope prediction shows the possibilities of antigenic variation.
Human respiratory syncytial virus (HRSV) is the main cause of severe respiratory illness in young children and elderly people. We investigated the genetic characteristics of the circulating HRSV subgroup A (HRSV-A) to determine the distribution of genotype ON1, which has a 72-nucleotide duplication in attachment G gene. We obtained 456 HRSV-A positive samples between October 2008 and February 2013, which were subjected to sequence analysis. The first ON1 genotype was discovered in August 2011 and 273 samples were identified as ON1 up to February 2013. The prevalence of the ON1 genotype increased rapidly from 17.4% in 2011–2012 to 94.6% in 2012–2013. The mean evolutionary rate of G protein was calculated as 3.275 × 10−3 nucleotide substitution/site/year and several positively selected sites for amino acid substitutions were located in the predicted epitope region. This basic and important information may facilitate a better understanding of HRSV epidemiology and evolution.
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Affiliation(s)
- You-Jin Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Dae-Won Kim
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Wan-Ji Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Mi-Ran Yun
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Ho Yeon Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Han Saem Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Hee-Dong Jung
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Kisoon Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea.
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Balmaks R, Ribakova I, Gardovska D, Kazaks A. Molecular epidemiology of human respiratory syncytial virus over three consecutive seasons in Latvia. J Med Virol 2013; 86:1971-82. [PMID: 24301088 DOI: 10.1002/jmv.23855] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2013] [Indexed: 11/06/2022]
Abstract
Lower respiratory tract infections caused by the human respiratory syncytial virus (HRSV) represent an immense burden of the disease, especially in young children. This study aimed to investigate the evolutionary history of HRSV strains isolated in the Children's Clinical University Hospital (Riga, Latvia) over three consecutive HRSV seasons. Of 207 samples from children hospitalized with lower respiratory tract infections, 88 (42.5%) tested positive for HRSV by RT-PCR. The seasonal activity started and peaked later than the average for the Northern hemisphere. Patients with HRSV lower respiratory tract infection were significantly younger than patients not infected with HRSV. HRSV-A viruses predominated for two consecutive seasons and were followed by an HRSV-B dominant season. Phylogenetic analysis based on glycoprotein G gene partial sequences revealed that viruses of both groups belonged to the worldwide dominant genotypes NA1 (HRSV-A) and BA-IV (HRSV-B). High diversity of this gene was driven only partially by selection pressure, as only two positively selected sites were identified in each group. Two of the HRSV-A isolates in this study contained a 72-nt duplication in the C-terminal end of the G gene (genotype ON1) that was first described in Canada in the 2010-2011 season. Initial spatial and temporal dynamics of this novel genotype were reconstructed by discrete phylogeographic analysis. Fifteen years after acquiring comparable 60-nt duplication in the G gene, genotype BA lineages have replaced all other HRSV-B strains. However, the population size of genotype ON1 plateaued soon and even decreased slightly before the beginning of the 2012-2013 season.
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Affiliation(s)
- Reinis Balmaks
- Department of Pediatrics, Riga Stradins University, Riga, Latvia; Children's Clinical University Hospital, Riga, Latvia
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Choudhary M, Anand S, Wadhwa B, Chadha M. Genetic variability of human respiratory syncytial virus in Pune, Western India. INFECTION GENETICS AND EVOLUTION 2013; 20:369-77. [DOI: 10.1016/j.meegid.2013.09.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/16/2013] [Accepted: 09/26/2013] [Indexed: 10/26/2022]
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Auksornkitti V, Kamprasert N, Thongkomplew S, Suwannakarn K, Theamboonlers A, Samransamruajkij R, Poovorawan Y. Molecular characterization of human respiratory syncytial virus, 2010-2011: identification of genotype ON1 and a new subgroup B genotype in Thailand. Arch Virol 2013; 159:499-507. [DOI: 10.1007/s00705-013-1773-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/15/2013] [Indexed: 10/26/2022]
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Cui G, Zhu R, Qian Y, Deng J, Zhao L, Sun Y, Wang F. Genetic variation in attachment glycoprotein genes of human respiratory syncytial virus subgroups a and B in children in recent five consecutive years. PLoS One 2013; 8:e75020. [PMID: 24069376 PMCID: PMC3775769 DOI: 10.1371/journal.pone.0075020] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/08/2013] [Indexed: 11/19/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) outranks other viral agents as the cause of respiratory tract diseases in children worldwide. Molecular epidemiological study of the virus provides useful information for the development of globally effective vaccine. We investigated the circulating pattern and genetic variation in the attachment glycoprotein genes of HRSV in Beijing during 5 consecutive seasons from 2007 to 2012. Out of 19,942 tested specimens, 3,160 (15.8%) were HRSV antigen-positive. The incidence of HRSV infection in males was significantly higher than in females. Of the total 723 (23.1%) randomly selected HRSV antigen-positive samples, 462 (63.9%) and 239 (33.1%) samples were identified as subgroup A and B, respectively. Subgroups A and B co-circulated in the 5 consecutive HRSV seasons, which showed a shifting mixed pattern of subgroup dominance. Complete G gene sequences were obtained from 190 HRSV-A and 72 HRSV-B by PCR for phylogenetic analysis. Although 4 new genotypes, NA3 and NA4 for HRSV-A and BA-C and CB1 for HRSV-B, were identified here, they were not predominant; NA1 and BA9 were the prevailing HRSV-A and -B genotypes, respectively. We provide the first report of a 9 consecutive nucleotide insertion in 3 CB1 genotype strains. One Beijing strain of ON1 genotype with a 72 nucleotide insertion was found among samples collected in February 2012. The reversion of codon states in glycosylation sites to previous ones were found from HRSV strains in this study, suggesting an immune-escape strategy of this important virus.
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Affiliation(s)
- Guanglin Cui
- Laboratory of Virology, Peking University Capital Institute of Pediatrics Teaching Hospital, Beijing, China
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Runan Zhu
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Yuan Qian
- Laboratory of Virology, Peking University Capital Institute of Pediatrics Teaching Hospital, Beijing, China
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
- * E-mail:
| | - Jie Deng
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Linqing Zhao
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Yu Sun
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Fang Wang
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
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