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Piñana M, González-Sánchez A, Andrés C, Vila J, Creus-Costa A, Prats-Méndez I, Arnedo-Muñoz M, Saubi N, Esperalba J, Rando A, Nadal-Baron P, Quer J, González-López JJ, Soler-Palacín P, Martínez-Urtaza J, Larrosa N, Pumarola T, Antón A. Genomic evolution of human respiratory syncytial virus during a decade (2013-2023): bridging the path to monoclonal antibody surveillance. J Infect 2024; 88:106153. [PMID: 38588960 DOI: 10.1016/j.jinf.2024.106153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/18/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES This study investigated the prevalence, genetic diversity, and evolution of human respiratory syncytial virus (HRSV) in Barcelona from 2013 to 2023. METHODS Respiratory specimens from patients with RTI suspicion at Hospital Universitari Vall d'Hebron were collected from October 2013 to May 2023 for laboratory-confirmation of respiratory viruses. Next-generation sequencing was performed in randomly-selected samples with Illumina technology. Phylogenetic analyses of whole genome sequences were performed with BEAST v1.10.4. Signals of selection and evolutionary pressures were inferred by population dynamics and evolutionary analyses. Mutations in major surface proteins were genetic and structurally characterised, emphasizing those within antigenic epitopes. RESULTS Analyzing 139,625 samples, 5.3% were HRSV-positive (3008 HRSV-A, 3882 HRSV-B, 56 HRSV-A and -B, and 495 unsubtyped HRSV), with a higher prevalence observed in the paediatric population. Pandemic-related shifts in seasonal patterns returned to normal in 2022-2023. A total of 198 whole-genome sequences were obtained for HRSV-A (6.6% of the HRSV-A positive samples) belonging to GA2.3.5 lineage. For HRSV-B, 167 samples were sequenced (4.3% of the HRSV-B positive samples), belonging to GB5.0.2, GB5.0.4a and GB5.0.5a. HRSV-B exhibited a higher evolution rate. Post-SARS-CoV-2 pandemic, both subtypes showed increased evolutionary rates and decreased effective population size initially, followed by a sharp increase. Analyses indicated negative selective pressure on HRSV. Mutations in antigenic epitopes, including S276N and M274I in palivizumab-targeted site II, and I206M, Q209R, and S211N in nirsevimab-targeted site Ø, were identified. DISCUSSION Particularly in the context of the large-scale use in 2023-2024 season of nirsevimab, continuous epidemiological and genomic surveillance is crucial.
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Affiliation(s)
- Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain; CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
| | - Alejandra González-Sánchez
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain; CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Department of Genetics and Microbiology, School of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain; CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Jorgina Vila
- Paediatric Infectious Diseases and Immunodeficiencies Unit, Children's Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain; Infection and Immunity Research Group, Vall d'Hebron Institut de Recerca, Barcelona, Catalonia, Spain; Paediatric Hospitalization Unit, Children's Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Anna Creus-Costa
- Paediatric Infectious Diseases and Immunodeficiencies Unit, Children's Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Ignasi Prats-Méndez
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Arnedo-Muñoz
- Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Narcís Saubi
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain; CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Juliana Esperalba
- Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ariadna Rando
- Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Patricia Nadal-Baron
- Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Juan José González-López
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Soler-Palacín
- Infection and Immunity Research Group, Vall d'Hebron Institut de Recerca, Barcelona, Catalonia, Spain; Paediatric Hospitalization Unit, Children's Hospital, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain; Department of Paediatrics, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Jaime Martínez-Urtaza
- Department of Genetics and Microbiology, School of Biosciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Nieves Larrosa
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain; Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain; CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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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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3
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Zhou X, Jiang M, Wang F, Qian Y, Song Q, Sun Y, Zhu R, Wang F, Qu D, Cao L, Ma L, Xu Y, De R, Zhao L. Immune escaping of the novel genotypes of human respiratory syncytial virus based on gene sequence variation. Front Immunol 2023; 13:1084139. [PMID: 36703972 PMCID: PMC9871593 DOI: 10.3389/fimmu.2022.1084139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Purpose Immune escaping from host herd immunity has been related to changes in viral genomic sequences. The study aimed to understand the diverse immune responses to different subtypes or genotypes of human respiratory syncytial virus (RSV) in pediatric patients. Methods The genomic sequences of different subtypes or RSV genotypes, isolated from Beijing patients, were sequenced and systematically analyzed. Specifically, the antiviral effects of Palivizumab and the cross-reactivity of human sera from RSV-positive patients to different subtypes or genotypes of RSV were determined. Then, the level of 38 cytokines and chemokines in respiratory and serum samples from RSV-positive patients was evaluated. Results The highest nucleotide and amino acid variations and the secondary and tertiary structure diversities among different subtypes or genotypes of RSV were found in G, especially for genotype ON1 with a 72bp-insertion compared to NA1 in subtype A, while more mutations of F protein were found in the NH-2 terminal, including the antigenic site II, the target of Palivizumab, containing one change N276S. Palivizumab inhibited subtype A with higher efficiency than subtype B and had stronger inhibitory effects on the reference strains than on isolated strains. However, RSV-positive sera had stronger inhibitory effects on the strains in the same subtypes or genotypes of RSV. The level of IFN-α2, IL-1α, and IL-1β in respiratory specimens from patients with NA1 was lower than those with ON1, while there were higher TNFα, IFNγ, IL-1α, and IL-1β in the first serum samples from patients with ON1 compared to those with BA9 of subtype B. Conclusions Diverse host immune responses were correlated with differential subtypes and genotypes of RSV in pediatric patients, demonstrating the impact of viral genetics on host immunity.
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Affiliation(s)
- Xiaohe Zhou
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Mingli Jiang
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Fengjie Wang
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Yuan Qian
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Qinwei Song
- Clinical Laboratory, Affiliated Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Yu Sun
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Runan Zhu
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Fang Wang
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Dong Qu
- Intensive Care Unit, Affiliated Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Ling Cao
- Department of Respiratory, Affiliated Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Lijuan Ma
- Clinical Laboratory, Affiliated Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Yanpeng Xu
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Ri De
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China,*Correspondence: Linqing Zhao, ; Ri De,
| | - Linqing Zhao
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China,Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China,*Correspondence: Linqing Zhao, ; Ri De,
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Jiang M, Xu Y, Wu H, Zhu R, Sun Y, Chen D, Wang F, Zhou Y, Guo Q, Wu A, Qian Y, Zhou H, Zhao L. Changes in endemic patterns of respiratory syncytial virus infection in pediatric patients under the pressure of nonpharmaceutical interventions for COVID-19 in Beijing, China. J Med Virol 2023; 95:e28411. [PMID: 36524893 PMCID: PMC9878212 DOI: 10.1002/jmv.28411] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
A series of nonpharmaceutical interventions (NPIs) was launched in Beijing, China, on January 24, 2020, to control coronavirus disease 2019. To reveal the roles of NPIs on the respiratory syncytial virus (RSV), respiratory specimens collected from children with acute respiratory tract infection between July 2017 and Dec 2021 in Beijing were screened by capillary electrophoresis-based multiplex PCR (CEMP) assay. Specimens positive for RSV were subjected to a polymerase chain reaction (PCR) and genotyped by G gene sequencing and phylogenetic analysis using iqtree v1.6.12. The parallel and fixed (paraFix) mutations were analyzed with the R package sitePath. Clinical data were compared using SPSS 22.0 software. Before NPIs launched, each RSV endemic season started from October/November to February/March of the next year in Beijing. After that, the RSV positive rate abruptly dropped from 31.93% in January to 4.39% in February 2020; then, a dormant state with RSV positive rates ≤1% from March to September, a nearly dormant state in October (2.85%) and November (2.98%) and a delayed endemic season in 2020, and abnormal RSV positive rates remaining at approximately 10% in summer until September 2021 were detected. Finally, an endemic RSV season returned in October 2021. There was a game between Subtypes A and B, and RSV-A replaced RSV-B in July 2021 to become the dominant subtype. Six RSV-A and eight RSV-B paraFix mutations were identified on G. The percentage of severe pneumonia patients decreased to 40.51% after NPIs launched. NPIs launched in Beijing seriously interfered with the endemic season of RSV.
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Affiliation(s)
- Ming‐Li Jiang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina,Graduate School of Peking Union Medical CollegeBeijingChina
| | - Yan‐Peng Xu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Hui Wu
- Institute of Systems MedicineChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina,Suzhou Institute of Systems MedicineSuzhouChina
| | - Ru‐Nan Zhu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Yu Sun
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Dong‐Mei Chen
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Fang Wang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Yu‐Tong Zhou
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Qi Guo
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Aiping Wu
- Institute of Systems MedicineChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina,Suzhou Institute of Systems MedicineSuzhouChina
| | - Yuan Qian
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina
| | - Hang‐Yu Zhou
- Institute of Systems MedicineChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina,Suzhou Institute of Systems MedicineSuzhouChina
| | - Lin‐Qing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijingChina,Graduate School of Peking Union Medical CollegeBeijingChina
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Sun YP, Lei SY, Wang YB, Wang YZ, Qiang HS, Yin YF, Jiang ZM, Zhu M, Chen XL, Ye HM, Zheng ZZ, Xia NS. Molecular Evolution of Attachment Glycoprotein (G) and Fusion Protein (F) Genes of Respiratory Syncytial Virus ON1 and BA9 Strains in Xiamen, China. Microbiol Spectr 2022; 10:e0208321. [PMID: 35311585 PMCID: PMC9045328 DOI: 10.1128/spectrum.02083-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/23/2022] [Indexed: 11/20/2022] Open
Abstract
Monitoring viral transmission and analyzing the genetic diversity of a virus are imperative to better understand its evolutionary history and the mechanism driving its evolution and spread. Especially, effective monitoring of key antigenic mutations and immune escape variants caused by these mutations has great scientific importance. Thus, to further understand the molecular evolutionary dynamics of respiratory syncytial virus (RSV) circulating in China, we analyzed nasopharyngeal swab specimens derived from hospitalized children ≤5 years old with acute respiratory tract infections (ARIs) in Xiamen during 2016 to 2019. We found that infants under 6 months of age (52.0%) were the main population with RSV infection. The prevalent pattern "BBAA" of RSV was observed during the epidemic seasons. RSV ON1 and BA9 genotypes were the dominant circulating strains in Xiamen. Interestingly, we observed four Xiamen-specific amino acid substitution combinations in the G protein and several amino acid mutations primarily occurring at antigenic sites Ø and V in the F protein. Our analyses suggest that introduction of new viruses and local evolution are shaping the diversification of RSV strains in Xiamen. This study provides new insights on the evolution and spread of the ON1 and BA9 genotypes at local and global scales. IMPORTANCE Monitoring the amino acid diversity of the RSV G and F genes helps us to find the novel genotypes, key antigenic mutations affecting antigenicity, or neutralizing antibody-resistant variants produced by natural evolution. In this study, we analyzed the molecular evolution of G and F genes from RSV strains circulating in Xiamen, China. These data provide new insights on local and global transmission and could inform the development of control measures for RSV infections.
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Affiliation(s)
- Yong-Peng Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Si-Yu Lei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Ying-Bin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Yi-Zhen Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Hong-Sheng Qiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Yi-Fan Yin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Ze-Min Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Min Zhu
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiao-Li Chen
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Hui-Ming Ye
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Zi-Zheng Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Ning-Shao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
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Determination of genetic characterization and circulation pattern of Respiratory Syncytial Virus (RSV) in children with a respiratory infection, Tehran, Iran, during 2018-2019. Virus Res 2021; 305:198564. [PMID: 34530047 DOI: 10.1016/j.virusres.2021.198564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/01/2021] [Accepted: 09/05/2021] [Indexed: 11/21/2022]
Abstract
The RSV-associated disease accounts for a significant health burden particularly in infants and young children who need to be hospitalized. Since continuous surveillance of circulating RSV genotypes is crucial worldwide, this study aimed to investigate the genetic diversity of RSV circulating strains causing upper or lower acute respiratory infection. Our attention was geared towards studying the cases hospitalized or outpatient in children younger than 2 years of age in Iran during 2018/2019. In this study, nasopharyngeal swabs collected from 206 children who presented with respiratory infection symptoms, were admitted to the referral pediatric ward of Bahrami children's hospital in Tehran, Iran. RSV-positive samples were detected via Nested RT-PCR. The glycoprotein gene was sequenced, and virus genotypes were confirmed through phylogenetic analysis by the MEGA X program. A total of 74 (35.92%) samples tested positive for RSV. Among them, sequencing was done in 10 specimens from 2018 (RSV-A: RSV-B=4:6) and 19 specimens from 2019 (RSV-A: RSV-B=16:3). According to phylogenetic analysis, all RSV-A strains were assigned as ON1 genotype and RSV-B strains were assigned as BA9 genotype. A new N-glycosylation site in Iranian BA9 and positive selection in ON1 genotype was observed. Phylogenetic characterization of strains in the current study revealed co-circulation of ON1 and BA9 as the only prevalent genotypes of both RSV-A and -B groups.
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Evolutionary dynamics of group A and B respiratory syncytial virus in China, 2009-2018. Arch Virol 2021; 166:2407-2418. [PMID: 34131849 DOI: 10.1007/s00705-021-05139-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Respiratory syncytial virus (RSV) is a major cause of acute respiratory tract infections in children and is a public health threat globally. To investigate the spatiotemporal dynamics of RSV evolution, we performed systematic phylogenetic analysis using all available sequences from the GenBank database, together with sequences from Shanghai, China. Both RSV-A and RSV-B appear to have originated in North America, with an inferred origin time of 1954.0 (1938.7-1967.6) and 1969.7 (1962.6-1975.5), respectively. BA-like strains of RSV-B, with a 60-nt insertion, and the ON1 strain of RSV-A, with a 72-nt insertion, emerged in 1997.6 (1996.2-1998.6) and 2010.1 (2009.1-2010.3), respectively. Since their origin, both genotypes have gradually replaced the former circulating genotypes to become the dominant strain. The population dynamic of RSV-A showed a seasonal epidemic pattern with obvious expansion in the periods of 2006-2007, 2010-2011, 2011-2012, and 2013-2014. Thirty fixed amino acid substitutions were identified during the divergence of NA4 from GA1 genotypes of RSV-A, and 13 were found during the divergence of SAB4 from GB1 of RSV-B. Importantly, ongoing evolution has occurred since the emergence of ON1, including four amino acid substitutions (I208L, E232G, T253K, and P314L). RSV-A genotypes GA5, NA4, NA1, and ON1 and RSV-B genotypes CB1, SAB4, BA-C, BA10, BA7, and BA9 were co-circulating in China from 2005 to 2015. In particular, RSV-A genotype ON1 was first detected in China in 2011, and it completely replaced GA2 to become the predominant strain after 2016. These data provide important insights into the evolution and epidemiology of RSV.
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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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Fall A, Elawar F, Hodcroft EB, Jallow MM, Toure CT, Barry MA, Kiori DE, Sy S, Diaw Y, Goudiaby D, Niang MN, Dia N. Genetic diversity and evolutionary dynamics of respiratory syncytial virus over eleven consecutive years of surveillance in Senegal. INFECTION GENETICS AND EVOLUTION 2021; 91:104864. [PMID: 33866019 DOI: 10.1016/j.meegid.2021.104864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Amary Fall
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Farah Elawar
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Mamadou Malado Jallow
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Cheikh Talibouya Toure
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Mamadou A Barry
- Unit Epidemiology of Infectious Diseases, Institute Pasteur of Dakar, Senegal.
| | | | - Sara Sy
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Yague Diaw
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | | | | | - Ndongo Dia
- Virology Department, Institute Pasteur of Dakar, Senegal.
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Respiratory syncytial virus B sequence analysis reveals a novel early genotype. Sci Rep 2021; 11:3452. [PMID: 33568737 PMCID: PMC7876121 DOI: 10.1038/s41598-021-83079-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.
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11
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Surges of hospital-based rhinovirus infection during the 2020 coronavirus disease-19 (COVID-19) pandemic in Beijing, China. World J Pediatr 2021; 17:590-596. [PMID: 34713393 PMCID: PMC8552974 DOI: 10.1007/s12519-021-00477-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/17/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND A series of public health preventive measures has been widely implemented in Beijing to control the coronavirus disease-19 (COVID-19) pandemic since January 2020. An evaluation of the effects of these preventive measures on the spread of other respiratory viruses is necessary. METHODS Respiratory specimens collected from children with acute respiratory infections were tested by NxTAG™ respiratory pathogen panel assays during January 2017 and December 2020. Specimens characterized as rhinoviruses (RVs) were sequenced to identify the RV species and types. Then, the epidemiology results of respiratory pathogens in 2020 were compared with those from 2017 to 2019 using SPSS statistics 22.0. RESULTS The positive rates of adenovirus (ADV), influenza virus (flu), RVs, and respiratory syncytial virus (RSV) dropped abruptly by 86.31%, 94.67%, 94.59%, and 92.17%, respectively, from February to May 2020, compared with the average level in the same period during 2017-2019. Positive rates of RVs then steeply increased from June 2020 (13.77%), to an apex (37.25%) in August 2020, significantly higher than the average rates (22.51%) in August 2017-2019 (P = 0.005). The increase, especially in group ≥ 3 years, was accompanied by the reopening of schools and kindergartens after the 23rd and 24th week of 2020 in Beijing. CONCLUSIONS Whereas the abrupt drop in viral pathogen positive rates from February to May 2020 revealed the remarkable effects of the COVID-19 preventive measures, the sharp increase in positive rates of RVs from the 23rd week of 2020 might be explained by the reopening of schools and kindergartens in Beijing.
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Malekshahi SS, Samieipour Y, Rahbarimanesh AA, Izadi A, Ghavami N, Razaghipour S, Naseri M, Mokhtari-Azad T, Salimi V. Genetic characterization of G protein in respiratory syncytial virus ON-1 genotype in Tehran. Future Virol 2020. [DOI: 10.2217/fvl-2019-0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Aim: We investigated the genetic characterization of the respiratory syncytial virus (RSV) ON-1 genotypes and their different lineages based on the G gene among children <2 years of age presenting with acute respiratory tract infections in Tehran, Iran. Materials & methods: A phylogenetic tree from the Iranian samples and ON-1 strains of various parts of the world were constructed. The amino acid composition of the RSV G protein of the ON-1 genotype was mapped. Results: Human RSV ON-1 genotypes from the Iranian samples clustered in three lineages. The most common amino acid substitutions were as follows: X218Q, I240S, L289P, Y304H and L310P. Conclusion: Continuing molecular epidemiological surveys in other regions of Iran will provide deeper insight into the nature of this replacement of the dominant RSV genotype from GA2 to ON-1 in Iran.
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Affiliation(s)
| | - Yazdan Samieipour
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Anahita Izadi
- Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nastaran Ghavami
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Razaghipour
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Naseri
- 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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Jagusic M, Slovic A, Ivancic-Jelecki J, Ljubin-Sternak S, Vilibić-Čavlek T, Tabain I, Forcic D. Molecular epidemiology of human respiratory syncytial virus and human metapneumovirus in hospitalized children with acute respiratory infections in Croatia, 2014-2017. INFECTION GENETICS AND EVOLUTION 2019; 76:104039. [PMID: 31521788 DOI: 10.1016/j.meegid.2019.104039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 01/09/2023]
Abstract
Acute respiratory infection (ARI) is the most common infection in children under 5 years of age and it is frequently caused by two pneumoviruses, human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV). Epidemic seasons of these viruses overlap and disease manifestations are highly similar, including severe lower ARI such as bronchiolitis or pneumonia. Reinfections with pneumoviruses are frequent and limited prevention treatment is available. Genetic diversity of HRSV and HMPV strains circulating in Croatia was monitored during four consecutive years (2014-2017). Co-circulation of multiple lineages was observed for both viruses. Within HRSV group A, ON1 strains gained strong predominance during the 4-year period, while previously dominant genotype NA1 was detected only sporadically. Similarly, newly occurring HMPV genotype A2c gained predominance over genotype A2b during this period, resulting in all infection in 2017 being caused by A2c. Along with phylogenetic analysis based on the commonly used fragments for detection and genotyping of these viruses, full length G and SH genes were also analysed. Evolutionary dynamics showed that inferred substitution rates of HRSV and HMPV are between 2.51 × 10-3 and 3.61 × 10-3 substitutions/site/year. This study established presence of recently described HMPV strains containing large duplications in the G gene in Croatia. Viruses with either of the two duplications belong to a subcluster A2c, which has completely replaced all other group A subclusters in 2017.
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Affiliation(s)
- M Jagusic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia
| | - A Slovic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia.
| | - J Ivancic-Jelecki
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia
| | - S Ljubin-Sternak
- Dr. Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; University of Zagreb School of Medicine, Zagreb, Croatia
| | - T Vilibić-Čavlek
- University of Zagreb School of Medicine, Zagreb, Croatia; Croatian National Institute of Public Health, Zagreb, Croatia
| | - I Tabain
- Croatian National Institute of Public Health, Zagreb, Croatia
| | - D Forcic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia
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