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Fu Y, Li F, Zhu Y, Huang L, Li Q, Zhang H, Zhong L, Zhang H, Luo ZX, Lu G, Deng J, Cao L, Wu Y, Jin R, Li L, Xu L, Chen X, Xie Z. A multi-center study on genetic variations in the fusion protein of respiratory syncytial virus from children with Acute Lower Respiratory Tract Infections in China during 2017-2021. Virol Sin 2024:S1995-820X(24)00141-X. [PMID: 39265703 DOI: 10.1016/j.virs.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 09/09/2024] [Indexed: 09/14/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a significant cause of acute lower respiratory tract infection (ALRTI) in children under five years of age. Between 2017 and 2021, 396 complete sequences of the RSV F gene were obtained from 500 RSV-positive throat swabs collected from ten hospitals across nine provinces in China. In addition, 151 sequences from China were sourced from GenBank and GISAID, making a total of 549 RSV F gene sequences subjected to analysis. Phylogenetic and genetic diversity analyses revealed that the RSV F genes circulating in China from 2017 to 2021 have remained relatively conserved, although some amino acids (AAs) have undergone changes. AA mutations with frequencies ≥ 10% were identified at six sites and the p27 region: V384I (site I), N276S (site II), R213S (site Ø), and K124N (p27) for RSV A; F45L (site I), M152I/L172Q/S173L/I185V/K191R (site V), and R202Q/I206M/Q209R (site Ø) for RSV B. Comparing mutational frequencies in RSV-F before and after 2020 revealed minor changes for RSV A, while the K191R, I206M, and Q209R frequencies increased by over 10% in RSV B. Notably, the nirsevimab-resistant mutation, S211N in RSV B, increased in frequency from 0% to 1.15%. Both representative strains aligned with the predicted RSV-F structures of their respective prototypes exhibited similar conformations, with low root-mean-square deviation values. These results could provide foundational data from China for the development of RSV mAbs and vaccines.
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Affiliation(s)
- Yiliang Fu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China
| | - Fei Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China
| | - Luci Huang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China
| | - Qiuping Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China
| | - Hanwen Zhang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China
| | - Lili Zhong
- Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Hailin Zhang
- Department of Children's Respiration disease, the Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zheng-Xiu Luo
- Department of Respiratory Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Gen Lu
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jikui Deng
- Department of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Ying Wu
- Department of Clinical Laboratory Medicine, National Children's Medical Center, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Rong Jin
- Guiyang Maternal and Child Health Hospital, Guiyang 550003, China
| | - Lei Li
- Yinchuan Maternal and Child Health Care Hospital, Yinchuan 750001, China
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China
| | - Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China.
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045 China; Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, 2019RU016 China.
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Characterisation of RSV Fusion Proteins from South African Patients with RSV Disease, 2019 to 2020. Viruses 2022; 14:v14112321. [PMID: 36366419 PMCID: PMC9698603 DOI: 10.3390/v14112321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022] Open
Abstract
Respiratory syncytial virus (RSV) is classified into RSV-A and RSV-B, which are further classified into genotypes based on variability in the G gene. The fusion (F) protein is highly conserved; however, variability within antigenic sites has been reported. This study aimed to characterise F proteins from RSV strains detected in South Africa from 2019 to 2020. Patients of all ages, from whom respiratory samples were submitted to the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic Hospital, South Africa during 2019 to 2020, were included. Complete RSV F genes were amplified for next-generation sequencing. MEGA X software was used for phylogenetic analysis. The overall prevalence of RSV was 5.8% (101/1734). Among 101 RSV positive samples only 69.3% (70/101) were available for characterization of the RSV F protein gene. Among cases included for F gene characterisation, viral co-infections were observed in 50% (35/70) and 25.7% (18/70) were admitted to intensive care units (ICU). About 74.2% (23/31) of F gene sequences cluster with other African NA1/ON1 genotypes. At antigenic site I, the V384I mutation was replaced by V384T in South African strains. The S275F mutation was seen in a single South African strain. The N120 N-linked glycosylation site was present in 25.8% (8/31) of RSV-A F proteins described in this study. For the first time, we detected the rare S275F mutation that is associated with palivizumab resistance.
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Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia. Genes (Basel) 2020; 11:genes11111323. [PMID: 33182267 PMCID: PMC7695323 DOI: 10.3390/genes11111323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial virus (HRSV) is a main cause of hospital admission for lower respiratory tract infection. In previous studies from Saudi Arabia, higher prevalence of the NA1 genotype in group A was observed from Riyadh and Taif. This study recruited respiratory cases from Jeddah during January to December, 2017. RSV represented 13.4% in the recruited cases with 64% of them belonging to group A and 36% to group B. All group A cases in this study were ON1 type characterized by duplication of 72 nucleotides, 24 amino acids in the C-terminal in the second hypervariable region of the G gene. In addition, for group B all of the cases were clustered under BA9, which had uniquely characterized as duplication of 60 nucleotides in the G protein. Our sequences showed similarity with earlier sequences from Saudi Arabia, Kuwait, Thailand, South Africa, Spain, the USA and Cyprus. Some amino acid substitutions in the investigated sequences would cause a change in potential O-glycosylation and N-glycosylation profiles from prototype ON1. The predominance of the ON1 and BA9 genotype of RSV-A in Jeddah compared to previous Saudi studies showing predominance of the NA1 genotype for group A. This difference in genotype prevalence could be due to fast spread of the ON1 genotype worldwide or due to the flux of travelers through Jeddah during hajj/umrah compared to Riyadh and Taif. This shift in genotype distribution requires continuous surveillance for genetic characterization of circulating respiratory infections including RSV. These findings may contribute to the understanding of RSV evolution and to the potential development of a vaccine against RSV.
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Joyce MG, Bao A, Chen M, Georgiev IS, Ou L, Bylund T, Druz A, Kong WP, Peng D, Rundlet EJ, Van Galen JG, Wang S, Yang Y, Zhang B, Chuang GY, McLellan JS, Graham BS, Mascola JR, Kwong PD. Crystal Structure and Immunogenicity of the DS-Cav1-Stabilized Fusion Glycoprotein From Respiratory Syncytial Virus Subtype B. Pathog Immun 2019; 4:294-323. [PMID: 31893251 PMCID: PMC6922093 DOI: 10.20411/pai.v4i2.338] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/21/2019] [Indexed: 11/23/2022] Open
Abstract
Background: Respiratory syncytial virus (RSV) subtypes, A and B, co-circulate in annual epidemics and alternate in dominance. We have shown that a subtype A RSV fusion (F) glycoprotein, stabilized in its prefusion conformation by DS-Cav1 mutations, is a promising RSV-vaccine immunogen, capable of boosting RSV-neutralizing titers in healthy adults. In both humans and vaccine-tested animals, neutralizing titers elicited by this subtype A DS-Cav1 immunogen were ~ 2- to 3-fold higher against the homologous subtype A virus than against the heterologous subtype B virus. Methods: To understand the molecular basis for this subtype difference, we introduced DS-Cav1 mutations into RSV strain B18537 F, determined the trimeric crystal structure, and carried out immunogenicity studies. Results: The B18537 DS-Cav1 F structure at 2-Å resolution afforded a precise delineation of prefusion F characteristics, including those of antigenic site Ø, a key trimer-apex site. Structural comparison with the subtype A prefusion F indicated 11% of surface residues to be different, with an alpha-carbon root-mean-square deviation (RMSD) of 1.2 Å; antigenic site Ø, however, differed in 23% of its surface residues and had an alpha-carbon RMSD of 2.2 Å. Immunization of vaccine-tested animals with DS-Cav1-stabilized B18537 F induced neutralizing responses ~100-fold higher than with postfusion B18537 F. Notably, elicited responses neutralized RSV subtypes A and B at similar levels and were directed towards both conserved equatorial and diverse apical regions. Conclusion: We propose that structural differences in apical and equatorial sites–coupled to differently focused immune responses–provide a molecular explanation for observed differences in elicited subtype A and B neutralizing responses.
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Affiliation(s)
- M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Amy Bao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Dongjun Peng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Emily J Rundlet
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Joseph G Van Galen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jason S McLellan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Respiratory syncytial, parainfluenza and influenza virus infection in young children with acute lower respiratory infection in rural Gambia. Sci Rep 2019; 9:17965. [PMID: 31784567 PMCID: PMC6884537 DOI: 10.1038/s41598-019-54059-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/23/2019] [Indexed: 01/06/2023] Open
Abstract
Respiratory viral infections contribute significantly to morbidity and mortality worldwide, but representative data from sub-Saharan Africa are needed to inform vaccination strategies. We conducted population-based surveillance in rural Gambia using standardized criteria to identify and investigate children with acute lower respiratory infection (ALRI). Naso- and oropharyngeal swabs were collected. Each month from February through December 2015, specimens from 50 children aged 2–23 months were randomly selected to test for respiratory syncytial (RSV), parainfluenza (PIV) and influenza viruses. The expected number of viral-associated ALRI cases in the population was estimated using statistical simulation that accounted for the sampling design. RSV G and F proteins and influenza hemagglutinin genes were sequenced. 2385 children with ALRI were enrolled, 519 were randomly selected for viral testing. One or more viruses were detected in 303/519 children (58.4%). RSV-A was detected in 237 and RSV-B in seven. The expected incidence of ALRI associated with RSV, PIV or influenza was 140 cases (95% CI, 131–149) per 1000 person-years; RSV incidence was 112 cases (95% CI, 102–122) per 1000 person-years. Multiple strains of RSV and influenza circulated during the year. RSV circulated throughout most of the year and was associated with eight times the number of ALRI cases compared to PIV or IV. Gambian RSV viruses were closely related to viruses detected in other continents. An effective RSV vaccination strategy could have a major impact on the burden of ALRI in this setting.
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Choi SH, Park KS, Kim YJ. Analysis of respiratory syncytial virus fusion protein from clinical isolates of Korean children in palivizumab era, 2009–2015. J Infect Chemother 2019; 25:514-519. [DOI: 10.1016/j.jiac.2019.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 02/07/2019] [Accepted: 02/20/2019] [Indexed: 02/07/2023]
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Malekshahi SS, Razaghipour S, Samieipoor Y, Hashemi FB, Manesh AAR, Izadi A, Faghihloo E, Ghavami N, Mokhtari-Azad T, Salimi V. Molecular characterization of the glycoprotein and fusion protein in human respiratory syncytial virus subgroup A: Emergence of ON-1 genotype in Iran. INFECTION GENETICS AND EVOLUTION 2019; 71:166-178. [PMID: 30946992 DOI: 10.1016/j.meegid.2019.03.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 03/05/2019] [Accepted: 03/29/2019] [Indexed: 12/20/2022]
Abstract
HRSV is a principle cause of infant hospitalization, childhood wheezing and a common pathogen in the elderly. Limited information exists regarding HRSV genotypes in Iran. In order to better understand HRSV strain diversity, we performed an in-depth evaluation of the genetic variability of the HRSV F protein detected in children under two years of age that, presented with acute respiratory symptoms during 2015-2016 in Tehran. A total of 180 nasopharyngeal swabs were evaluated. The HRSV positive samples were genotyped for G and F gene sequences using RT-PCR and sequencing methods. Phylogenetic analysis was performed using the neighbor-joining and maximum likelihood methods. Genetic and antigenic characteristics of the F gene, nucleotide and amino acids in significant positions and immune system binding regions, as well as the p-distance, positive/negative selection site, linear epitopes and glycosylation sites were investigated in all selected sequences. Among the 83 HRSV positive samples, the Fifty-five cases were successfully sequenced. All of them were classified as subgroup A and belonged to the ON-1 genotype, which possessed 72-nt duplication in the G gene. This study is the first report on the emergence of ON-1 in Iran. ON-1 Iranian sequences clustered in three lineages according to virus fusion (F) gene variations. F gene sequence analysis showed that all genetic changes in the isolates from Iran were base substitutions and no deletion/insertions were identified. The low dN/dS ratio and lack of positively selected sites showed that the fusion genes found in the strains from Iran are not under host selective pressure. Continuing and long-term molecular epidemiological surveys for early detection of circulating and newly emerging genotypes are necessary to gain a better understanding of their epidemic potential.
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Affiliation(s)
| | - Shaghayegh Razaghipour
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yazdan Samieipoor
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad B Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Anahita Izadi
- Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nastaran Ghavami
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Song J, Wang H, Ng TI, Cui A, Zhu S, Huang Y, Sun L, Yang Z, Yu D, Yu P, Zhang H, Zhang Y, Xu W. Sequence Analysis of the Fusion Protein Gene of Human Respiratory Syncytial Virus Circulating in China from 2003 to 2014. Sci Rep 2018; 8:17618. [PMID: 30514963 PMCID: PMC6279739 DOI: 10.1038/s41598-018-35894-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/09/2018] [Indexed: 11/09/2022] Open
Abstract
The human respiratory syncytial virus (HRSV) fusion (F) protein is important for HRSV infection, but few studies have examined the genetic diversity of the F gene from Chinese samples. In this study, a total of 330 HRSV F sequences collected from different regions of China between 2003 and 2014 were analyzed to understand their genetic characteristics. In addition, these sequences were compared with 1150 HRSV F sequences in Genbank from 18 other countries. In phylogenetic analysis, Chinese HRSV F sequences sorted into a number of clusters containing sequences from China as well as other countries. F sequences from different genotypes (as determined based on the G gene sequences) within a HRSV subgroup could be found in the same clusters in phylogenetic trees generated based on F gene sequences. Amino acid analysis showed that HRSV F sequences from China and other countries were highly conserved. Of interest, F protein sequences from all Chinese samples were completely conserved at the palivizumab binding site, thus predicting the susceptibility of these strains to this neutralizing antibody. In conclusion, HRSV F sequences from China between 2003 and 2014, similar to those from other countries, were highly conserved.
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Affiliation(s)
- Jinhua Song
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, National Health Commission of the People's Republic of China, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Huiling Wang
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, National Health Commission of the People's Republic of China, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | | | - Aili Cui
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, National Health Commission of the People's Republic of China, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuangli Zhu
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, National Health Commission of the People's Republic of China, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yanzhi Huang
- Jilin Children's Medical Center, Children's Hospital of Changchun, Changchun, People's Republic of China
| | - Liwei Sun
- Jilin Children's Medical Center, Children's Hospital of Changchun, Changchun, People's Republic of China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Deshan Yu
- Gansu Provincial Centers for Disease Control and Prevention, Lanzhou, People's Republic of China
| | - Pengbo Yu
- Shaanxi Provincial Centers for Disease Control and Prevention, Xian, People's Republic of China
| | - Hong Zhang
- Hunan Provincial Centers for Disease Control and Prevention, Changsha, People's Republic of China
| | - Yan Zhang
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, National Health Commission of the People's Republic of China, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China.
| | - Wenbo Xu
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, National Health Commission of the People's Republic of China, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China.
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9
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Okamoto M, Dapat CP, Sandagon AMD, Batangan-Nacion LP, Lirio IC, Tamaki R, Saito M, Saito-Obata M, Lupisan SP, Oshitani H. Molecular Characterization of Respiratory Syncytial Virus in Children With Repeated Infections With Subgroup B in the Philippines. J Infect Dis 2018; 218:1045-1053. [PMID: 29722817 PMCID: PMC6107742 DOI: 10.1093/infdis/jiy256] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/01/2018] [Indexed: 11/26/2022] Open
Abstract
Background Human respiratory syncytial virus (RSV) is the leading cause of severe acute respiratory infection in infants and young children, which is characterized by repeated infections. However, the role of amino acid substitutions in repeated infections remains unclear. Hence, this study aimed to elucidate the genetic characteristics of RSV in children with repeated infections using molecular analyses of F and G genes. Methods We conducted a cohort study of children younger than 5 years in the Philippines. We collected nasopharyngeal swabs from children with acute respiratory symptoms and compared F and G sequences between initial and subsequent RSV infections. Results We examined 1802 children from May 2014 to January 2016 and collected 3471 samples. Repeated infections were observed in 25 children, including 4 with homologous RSV-B reinfections. Viruses from the 4 pairs of homologous reinfections had amino acid substitutions in the G protein mostly at O-glycosylation sites, whereas changes in the F protein were identified at antigenic sites V (L173S) and θ (Q209K), considered essential epitopes for the prefusion conformation of the F protein. Conclusions Amino acid substitutions in G and F proteins of RSV-B might have led to antigenic changes, potentially contributing to homologous reinfections observed in this study.
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Affiliation(s)
- Michiko Okamoto
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Clyde P Dapat
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Ann Marie D Sandagon
- Tohoku-Research Institute for Tropical Medicine Collaborating Research Center on Emerging and Reemerging Infectious Diseases
| | | | - Irene C Lirio
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Raita Tamaki
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Mayuko Saito
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Mariko Saito-Obata
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Tohoku-Research Institute for Tropical Medicine Collaborating Research Center on Emerging and Reemerging Infectious Diseases
| | - Socorro P Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Hitoshi Oshitani
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
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10
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Chen X, Xu B, Guo J, Li C, An S, Zhou Y, Chen A, Deng L, Fu Z, Zhu Y, Liu C, Xu L, Wang W, Shen K, Xie Z. Genetic variations in the fusion protein of respiratory syncytial virus isolated from children hospitalized with community-acquired pneumonia in China. Sci Rep 2018. [PMID: 29540836 PMCID: PMC5852162 DOI: 10.1038/s41598-018-22826-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To identify the variations in fusion (F) protein gene of RSV in China, a molecular epidemiological study was conducted. A total of 553 RSV positive specimens were collected from 2338 pediatric patients hospitalized with community-acquired pneumonia during a multi-center study conducted during 2014–2016. A total of 252 samples (183 RSV A, 69 RSV B) were selected for F gene sequencing, and analyzed together with 142 F gene sequences downloaded from GenBank. The result showed that all the Chinese RSV A and RSV B strains could be divided respectively into three branches. Compared with RSV A/B prototype sequences respectively, there were significant amino acid (AA) mutations at multiple antigenic sites. For RSV A, changes were found at AA residues 122, 124, 125, 276 and 384, and for RSV B at AA residues 45, 116, 125, 172, 173 and 202. Variations in human histocompatibility leukocyte antigen-restricted CTL epitopes were also observed. In total, 56 amino acid differences for the complete F protein were found between the RSV A and B groups in China, while several mutations were only found in the RSV B strains during 2015–2016. The RSV F gene is relatively conserved in China, however, limited mutations are still occurring with time.
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Affiliation(s)
- Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Beijing Pediatric Research Institute, Beijing, 100045, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Baoping Xu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Jiayun Guo
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Beijing Pediatric Research Institute, Beijing, 100045, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Changchong Li
- The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shuhua An
- Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Yunlian Zhou
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Aihuan Chen
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Deng
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zhou Fu
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Beijing Pediatric Research Institute, Beijing, 100045, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Chunyan Liu
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Beijing Pediatric Research Institute, Beijing, 100045, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Beijing Pediatric Research Institute, Beijing, 100045, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Wei Wang
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Beijing Pediatric Research Institute, Beijing, 100045, China.,Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Kunling Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China.
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Beijing Pediatric Research Institute, Beijing, 100045, China. .,Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China.
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11
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Tang JW, Lam TT, Zaraket H, Lipkin WI, Drews SJ, Hatchette TF, Heraud JM, Koopmans MP. Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance. THE LANCET. INFECTIOUS DISEASES 2017; 17:e320-e326. [PMID: 28457597 PMCID: PMC7164797 DOI: 10.1016/s1473-3099(17)30238-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 01/06/2017] [Accepted: 02/07/2017] [Indexed: 01/13/2023]
Abstract
Together with influenza, the non-influenza RNA respiratory viruses (NIRVs), which include respiratory syncytial virus, parainfluenza viruses, coronavirus, rhinovirus, and human metapneumovirus, represent a considerable global health burden, as recognised by WHO's Battle against Respiratory Viruses initiative. By contrast with influenza viruses, little is known about the contemporaneous global diversity of these viruses, and the relevance of such for development of pharmaceutical interventions. Although far less advanced than for influenza, antiviral drugs and vaccines are in different stages of development for several of these viruses, but no interventions have been licensed. This scarcity of global genetic data represents a substantial knowledge gap and impediment to the eventual licensing of new antiviral drugs and vaccines for NIRVs. Enhanced genetic surveillance will assist and boost research and development into new antiviral drugs and vaccines for these viruses. Additionally, understanding the global diversity of respiratory viruses is also part of emerging disease preparedness, because non-human coronaviruses and paramyxoviruses have been listed as priority concerns in a recent WHO research and development blueprint initiative for emerging infectious diseases. In this Personal View, we explain further the rationale for expanding the genetic database of NIRVs and emphasise the need for greater investment in this area of research.
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Affiliation(s)
- Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK; Department of Infection, Inflammation and Immunity, University of Leicester, Leicester, UK.
| | - Tommy T Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology, and Microbiology, American University of Beirut, Beirut, Lebanon
| | - W Ian Lipkin
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Steven J Drews
- Alberta Provincial Laboratory for Public Health, University of Alberta, Edmonton, AB, Canada
| | - Todd F Hatchette
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
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12
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Oliveira DBL, Iwane MK, Prill MM, Weinberg GA, Williams JV, Griffin MR, Szilagyi PG, Edwards KM, Staat MA, Hall CB, Durigon EL, Erdman DD. Molecular characterization of respiratory syncytial viruses infecting children reported to have received palivizumab immunoprophylaxis. J Clin Virol 2015; 65:26-31. [PMID: 25766983 PMCID: PMC7172275 DOI: 10.1016/j.jcv.2015.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/17/2015] [Accepted: 01/23/2015] [Indexed: 11/08/2022]
Abstract
Palivizumab (PZ) immunoprophylaxis of high-risk children reduces RSV hospitalizations. PZ resistance mutations can result in RSV breakthrough infections in PZ recipients. PZ resistance mutations were identified in 10.2% of children reportedly receiving PZ. PZ resistance mutations did not account for the majority of PZ failures.
Background Respiratory syncytial virus (RSV) is a major cause of respiratory infections in children. Palivizumab (PZ) is the only RSV-specific immunoprophylaxis approved by the U.S. Food and Drug Administration. Mutations leading to amino acid substitutions in the PZ binding site of the RSV F protein have been associated with breakthrough RSV infections in patients receiving PZ. Objective To detect PZ resistance conferring mutations in RSV strains from children who received PZ. Study design Children aged ≤24 months on October 31 who were hospitalized or had outpatient visits for respiratory illness and/or fever during October–May 2001–2008 in 3 US counties were included. PZ receipt was obtained from parent interviews and medical records among children subsequently infected with RSV. Archived nasal/throat swab specimens were tested for RSV by real-time RT-PCR. The coding region of the PZ binding site of the RSV F protein was sequenced using both Sanger and pyrosequencing methods. Results Of 8762 enrolled children, 375 (4.3%) were tested for RSV and had a history of PZ receipt, of which 56 (14.9%) were RSV-positive and 45 of these had available archived specimens. Molecular typing identified 42 partial F gene sequences in specimens from 39 children: 19 single RSV subgroup A, 17 subgroup B and 3 mixed infections. Nucleotide substitutions were identified in 12/42 (28.6%) RSV strains. PZ resistance mutations were identified in 4 (10.2%) of the 39 children, of which one had documented PZ receipt. Conclusions Although RSV PZ resistance mutations were infrequent, most RSV-associated illnesses in children with a history of PZ receipt were not due to strain resistance.
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Affiliation(s)
| | - Marika K Iwane
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mila M Prill
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | | | | | - Mary A Staat
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Caroline B Hall
- University of Rochester School of Medicine, Rochester, NY, USA
| | - Edison L Durigon
- Institute of Biomedical Science, University of São Paulo, Brazil
| | - Dean D Erdman
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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13
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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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14
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Zhou L, Zheng S, Xiao Q, Ren L, Xie X, Luo J, Wang L, Huang A, Liu W, Liu E. Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children. BMC Infect Dis 2014; 14:424. [PMID: 25078257 PMCID: PMC4125703 DOI: 10.1186/1471-2334-14-424] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/15/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Human bocavirus is a newly discovered parvovirus. Multiple studies have confirmed the presence of human bocavirus1 (HBoV1) in respiratory tract samples of children. The viral load, presentation of single detection and its role as a causative agent of severe respiratory tract infections have not been thoroughly elucidated. METHODS We investigated the presence of HBoV1 by quantitative polymerase chain reaction (PCR) of nasopharyngeal aspirate specimens from 1229 children hospitalized for respiratory tract infections. The samples were analyzed for 15 respiratory viruses by PCR and 7 respiratory viruses by viral culture. RESULTS At least one virus was detected in 652 (53.1%) of 1229 children, and two or more viruses were detected in 266 (21.6%) children. HBoV1 was detected in 127 children (10.3%), in which 66/127 (52%) of the cases were the only HBoV1 virus detected. Seasonal variation was observed with a high HBoV1 infection rate in summer. A cutoff value of 107 copies/mL was used to distinguish high and low HBoV1 viral loads in the nasopharyngeal aspirates. High viral loads of HBoV1 were noted predominantly in the absence of other viral agents (28/39, 71.8%) whereas there was primarily co-detection in cases of low HBoV1 viral loads (50/88, 56.8%). There were no differences in the clinical symptoms and severity between HBoV1 single detection and co-detection. In cases of HBoV1 single detection, the high viral load group was more prevalent among children with dyspnea and wheezing than was the low viral load group (42.9% vs. 23.7%, P = 0.036; 60.7% vs. 31.6%, P = 0.018). In clinical severity, a significant difference was recorded (25.0% vs. 5.3%, P = 0.003) between high viral load and low viral load groups. Of the HBoV1 positive patients associated with severe respiratory tract infections, 10/18 (55.6%) patients belonged to the HBoV1 high viral load group, and 7/10 (70%) patients had cases of HBoV1 single detection. CONCLUSIONS HBoV1 at a high viral load is not frequently found in co-detection with other respiratory viruses, and a single detection with a high viral load could be an etiological agent of severe respiratory tract infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Enmei Liu
- Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, P, R, China.
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