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Hou M, Liu G, Meng C, Dong L, Fang Y, Wang L, Wang N, Cai C, Wang H. Circulation patterns and molecular characteristics of respiratory syncytial virus among hospitalized children in Tianjin, China, before and during the COVID-19 pandemic (2017-2022). Virol Sin 2024:S1995-820X(24)00114-7. [PMID: 39067791 DOI: 10.1016/j.virs.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/24/2024] [Indexed: 07/30/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the main pathogen that causes hospitalization for acute lower respiratory tract infections (ALRIs) in children. With the reopening of communities and schools, the resurgence of RSV in the COVID-19 post-pandemic era has become a major concern. To understand the circulation patterns and genotype variability of RSV in Tianjin before and during the COVID-19 pandemic, a total of 19,531 nasopharyngeal aspirate samples from hospitalized children in Tianjin from July 2017 to June 2022 were evaluated. Direct immunofluorescence and polymerase chain reaction (PCR) were used for screening RSV-positive samples and subtyping, respectively. Further analysis of mutations in the second hypervariable region (HVR2) of the G gene was performed through Sanger sequencing. Our results showed that 16.46% (3215/19,531) samples were RSV positive and a delayed increase in the RSV infection rates occurred in the winter season from December 2020 to February 2021, with the average RSV-positive rate of 35.77% (519/1451). The ON1, with H258Q and H266L substitutions, and the BA9, with T290I and T312I substitutions, are dominant strains that alternately circulate every 1-2 years in Tianjin, China, from July 2017 to June 2022. In addition, novel substitutions, such as N296Y, K221T, N230K, V251A in the BA9 genotype, and L226I in the ON1 genotype, emerged during the COVID-19 pandemic. Analysis of clinical characteristics indicated no significant differences between RSV-A and RSV-B groups. This study provides a theoretical basis for clinical prevention and treatment. However, further studies are needed to explore the regulatory mechanism of host immune responses to different lineages of ON1 and BA9 in the future.
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Affiliation(s)
- Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Guangping Liu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Chao Meng
- Department of Medical Laboratory, Tianjin Second People's Hospital, Tianjin, 300192, China
| | - Lili Dong
- Department of Respiratory, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, 300134, China
| | - Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Ning Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Hanjie Wang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China.
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Moumbeket Yifomnjou MH, Monamele GC, Modiyinji AF, Njankouo-Ripa M, Onana B, Njouom R. Genetic Diversity of Human Respiratory Syncytial Virus during COVID-19 Pandemic in Yaoundé, Cameroon, 2020-2021. Microorganisms 2024; 12:952. [PMID: 38792782 PMCID: PMC11123827 DOI: 10.3390/microorganisms12050952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Worldwide, human respiratory syncytial virus (HRSV) is a major cause of severe infections of the lower respiratory system, affecting individuals of all ages. This study investigated the genetic variability of HRSV during the COVID-19 outbreak in Yaoundé; nasopharyngeal samples positive for HRSV were collected from different age groups between July 2020 and October 2021. A semi-nested RT-PCR was performed on the second hypervariable region of the G gene of detected HRSV, followed by sequencing and phylogenetic assessment. Throughout the study, 40 (37.7%) of the 106 HRSV-positive samples successfully underwent G-gene amplification. HRSV A and HRSV B co-circulated at rates of 47.5% and 52.5%, respectively. HRSV A clustered in the GA2.3.5 genetic lineage (ON1) and HRSV B clustered in the GB5.0.5a genetic lineage (BA9). Differences in circulating genotypes were observed between pre- and post-pandemic years for HRSV A. Predictions revealed potential N-glycosylation sites at positions 237-318 of HRSV A and positions 228-232-294 of HRSV B. This study reports the molecular epidemiology of HRSV in Cameroon during the COVID-19 pandemic. It describes the exclusive co-circulation of two genetic lineages. These findings highlight the importance of implementing comprehensive molecular surveillance to prevent the unexpected emergence of other diseases.
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Affiliation(s)
- Moïse Henri Moumbeket Yifomnjou
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Gwladys Chavely Monamele
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Abdou Fatawou Modiyinji
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Mohamadou Njankouo-Ripa
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Boyomo Onana
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Richard Njouom
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
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Guo YJ, Wang BH, Li L, Li YL, Chu XL, Li W. Epidemiological and genetic characteristics of respiratory syncytial virus infection in children from Hangzhou after the peak of COVID-19. J Clin Virol 2023; 158:105354. [PMID: 36525852 PMCID: PMC9747354 DOI: 10.1016/j.jcv.2022.105354] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is one of the main pathogens that causes acute lower respiratory tract infection (ARTI) in infants. During the Coronavirus Disease 2019 (COVID-19) pandemic, although strict interventions have been implemented, RSV infection has not decreased. OBJECTIVES To study the epidemiological and genetic characteristics of RSV circulating in Hangzhou after the peak of COVID-19. METHODS A total of 1225 nasopharyngeal swabs were collected from outpatients with ARTIs from July 2021 to January 2022 in The Children's Hospital, Zhejiang University School of Medicine. RESULTS A total of 267 (21.79%) of the 1225 samples were RSV positive. There was no gender bias. However, an obvious age preference for infection was observed, and children aged 3-6 years were more susceptible, which was very different from previous RSV pandemic seasons. Phylogenetic analysis of 115 sequenced RSV isolates showed that all the RSV-A viruses belong to the ON1 subtype, which could be clustered into three clusters. While all the RSV-B viruses belong to BA9. Further analysis of the mutations highlights the fixation of ten mutations, which should be given extra attention regarding their biological properties. CONCLUSION The incidence of RSV infection in preschool children reported in this study is high. Phylogenetic analysis showed that the subtype A ON1 genotype was the dominant strain in Hangzhou from July 2021 to January 2022.
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Affiliation(s)
- Ya-jun Guo
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health. Hangzhou 310052, PR China
| | - Bing-han Wang
- School of Public Health, Zhejiang University School of Medicine, Hangzhou 310052, PR China
| | - Lin Li
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health. Hangzhou 310052, PR China
| | | | - Xiao-li Chu
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health. Hangzhou 310052, PR China
| | - Wei Li
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health. Hangzhou 310052, PR China.
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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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Chen X, Zhu Y, Wang W, Li C, An S, Lu G, Jin R, Xu B, Zhou Y, Chen A, Li L, Zhang M, Xie Z. A multi-center study on Molecular Epidemiology of Human Respiratory Syncytial Virus from Children with Acute Lower Respiratory Tract Infections in the Mainland of China between 2015 and 2019. Virol Sin 2021; 36:1475-1483. [PMID: 34398429 PMCID: PMC8365132 DOI: 10.1007/s12250-021-00430-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/18/2021] [Indexed: 11/25/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is a major pathogen of acute lower respiratory tract infection among young children. To investigate the prevalence and genetic characteristics of RSV in China, we performed a molecular epidemiological study during 2015-2019. A total of 964 RSV-positive specimens were identified from 5529 enrolled patients during a multi-center study. RSV subgroup A (RSV-A) was the predominant subgroup during this research period except in 2016. Totally, 535 sequences of the second hypervariable region (HVR-2) of the G gene were obtained. Combined with 182 Chinese sequences from GenBank, phylogenetic trees showed that 521 RSV-A sequences fell in genotypes ON1 (512), NA1 (6) and GA5 (3), respectively; while 196 RSV-B sequences fell in BA9 (193) and SAB4 (3). ON1 and BA9 were the only genotypes after December 2015. Genotypes ON1 and BA9 can be separated into 10 and 7 lineages, respectively. The HVR-2 of genotype ON1 had six amino acid changes with a frequency more than 10%, while two substitutions H258Q and H266L were co-occurrences. The HVR-2 of genotype BA9 had nine amino acid substitutions with a frequency more than 10%, while the sequences with T290I and T312I were all from 2018 to 2019. One N-glycosylation site at 237 was identified among ON1 sequences, while two N-glycosylation sites (296 and 310) were identified in the 60-nucleotide duplication region of BA9. To conclusion, ON1 and BA9 were the predominant genotypes in China during 2015-2019. For the genotypes ON1 and BA9, the G gene exhibited relatively high diversity and evolved continuously.
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Affiliation(s)
- 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, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, 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, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wei Wang
- 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, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Changchong Li
- The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Shuhua An
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Gen Lu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Rong Jin
- Guiyang Maternal and Child Health Hospital, Guiyang, 550003, China
| | - Baoping Xu
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Yunlian Zhou
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Aihuan Chen
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Lei Li
- Yinchuan Maternal and Child Health Care Hospital, Yinchuan, 750001, China
| | - Meng 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, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, 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, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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Next-generation sequencing of human respiratory syncytial virus subgroups A and B genomes. J Virol Methods 2021; 299:114335. [PMID: 34673119 DOI: 10.1016/j.jviromet.2021.114335] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/17/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and provides genomic information essential for antiviral and vaccine development. A 10-amplicon one-step RT-PCR assay and a 20-amplicon nested RT-PCR assay with enhanced sensitivity were developed to amplify whole HRSV genomes from samples containing high and low viral loads, respectively. Ninety-six HRSV-positive samples comprised of 58 clinical specimens and 38 virus isolates with Ct values ≤ 24 were amplified successfully using the 10-amplicon one-step RT-PCR method and multiplexed in a single MiSeq run. Genome coverage exceeded 99.3% for all 96 samples. The 20-amplicon nested RT-PCR NGS method was used to generate >99.6% HRSV full-length genome for 72 clinical specimens with Ct values ranging from 24 to 33. Phylogenetic analysis of the genome sequences obtained from the 130 clinical specimens revealed a wide diversity of HRSV genotypes demonstrating methodologic robustness.
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Yu JM, Fu YH, Peng XL, Zheng YP, He JS. Genetic diversity and molecular evolution of human respiratory syncytial virus A and B. Sci Rep 2021; 11:12941. [PMID: 34155268 PMCID: PMC8217232 DOI: 10.1038/s41598-021-92435-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial viruses (RSVs) are classified into two major groups (A and B) based on antigenic differences in the G glycoprotein. To investigate circulating characteristics and phylodynamic history of RSV, we analyzed the genetic variability and evolutionary pattern of RSVs from 1977 to 2019 in this study. The results revealed that there was no recombination event of intergroup. Single nucleotide polymorphisms (SNPs) were observed through the genome with the highest occurrence rate in the G gene. Five and six sites in G protein of RSV-A and RSV-B, respectively, were further identified with a strong positive selection. The mean evolutionary rates for RSV-A and -B were estimated to be 1.48 × 10–3 and 1.92 × 10–3 nucleotide substitutions/site/year, respectively. The Bayesian skyline plot showed a constant population size of RSV-A and a sharp expansion of population size of RSV-B since 2005, and an obvious decrease 5 years later, then became stable again. The total population size of RSVs showed a similar tendency to that of RSV-B. Time-scaled phylogeny suggested a temporal specificity of the RSV-genotypes. Monitoring nucleotide changes and analyzing evolution pattern for RSVs could give valuable insights for vaccine and therapy strategies against RSV infection.
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Affiliation(s)
- Jie-Mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yuan-Hui Fu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Xiang-Lei Peng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yan-Peng Zheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
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Komoyo GF, Yambiyo BM, Manirakiza A, Gody JC, Muller CP, Hübschen JM, Nakoune E, Snoeck CJ. Epidemiology and genetic characterization of respiratory syncytial virus in children with acute respiratory infections: Findings from the influenza sentinel surveillance network in Central African Republic, 2015 to 2018. Health Sci Rep 2021; 4:e298. [PMID: 34013070 PMCID: PMC8112815 DOI: 10.1002/hsr2.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND AND AIMS Respiratory syncytial virus (RSV) is one of the main viral pathogens causing acute respiratory infections in children under 5 years of age but has seldom been studied in Central African Republic (CAF). Taking advantage of the national influenza surveillance network in CAF, this study aimed at providing the first insights into RSV prevalence and seasonality over 4 years of surveillance and the clinical manifestations of RSV in this population in CAF. METHODS A total of 3903 children under 5 years matching the influenza-like illness (ILI, 68.5%) or severe acute respiratory infection (SARI, 31.5%) case definitions were recruited from January 2015 to December 2018. The presence of RSV viral RNA in nasopharyngeal samples was assessed by RT-PCR, followed by RSV-A and RSV-B typing and Sanger sequencing on a subset of samples. Phylogenetic analyses were carried on partial G protein sequences. Associations between RSV and demographic or clinical manifestations were investigated by statistical analyses. RESULTS RSV prevalence was significantly higher in infants <6 months (13.4%), in hospitalized children (13.3% vs 5.5%) and in male patients (9.5% vs 6.4%). An overall prevalence of RSV of 8.0% in the period of 2015 to 2018 was shown, with significant annual (6.4%-10.6%) and seasonal (12.7% in rainy season vs 3.0% in dry season) fluctuations. While RSV seasons in 2015, 2016, and 2018 were relatively similar, 2017 showed deviations from the overall patterns with significantly higher RSV circulation and an outbreak peak 3 to 5 months earlier. Concomitant circulation of RSV-A and RSV-B with an alternating predominance of RSV-A and RSV-B strains and temporal RSV-A genotype replacement from NA1 to ON1 was observed. CONCLUSION This study represents the first in-depth epidemiological analysis of RSV in CAF and provides first insights into RSV genetic diversity and seasonality in the country.
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Affiliation(s)
- Giscard F. Komoyo
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
- Ecole Doctorale d'Infectiologie Tropicale de Franceville, GabonFrancevilleGabon
| | - Brice M. Yambiyo
- Service d'épidémiologieInstitut Pasteur de BanguiBanguiCentral African Republic
| | | | - Jean C. Gody
- Complexe pédiatrique de BanguiCentre National Hospitalier Universitaire de BanguiBanguiCentral African Republic
| | - Claude P. Muller
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Judith M. Hübschen
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Emmanuel Nakoune
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
| | - Chantal J. Snoeck
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
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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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Systematic Review of the Respiratory Syncytial Virus (RSV) Prevalence, Genotype Distribution, and Seasonality in Children from the Middle East and North Africa (MENA) Region. Microorganisms 2020; 8:microorganisms8050713. [PMID: 32403364 PMCID: PMC7284433 DOI: 10.3390/microorganisms8050713] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most common viruses to infect children worldwide and is the leading cause of lower respiratory tract illness (LRI) in infants. This study aimed to conduct a systematic review by collecting and reviewing all the published knowledge about the epidemiology of RSV in the Middle East and North Africa (MENA) region. Therefore, we systematically searched four databases; Embase, Medline, Scopus, and Cochrane databases from 2001 to 2019 to collect all the information related to the RSV prevalence, genotype distribution, and seasonality in children in MENA region. Our search strategy identified 598 studies, of which 83 met our inclusion criteria, which cover the past 19 years (2000–2019). Odds ratio (OR) and confidence interval (CI) were calculated to measure the association between RSV prevalence, gender, and age distribution. An overall prevalence of 24.4% (n = 17,106/69,981) of respiratory infections was recorded for RSV. The highest RSV prevalence was reported in Jordan (64%, during 2006–2007) and Israel (56%, 2005–2006). RSV A subgroup was more prevalent (62.9%; OR = 2.9, 95%CI = 2.64–3.13) than RSV B. RSV was most prevalent in children who were less than 12 months old (68.6%; OR = 4.7, 95%CI = 2.6–8.6) and was higher in males (59.6%; OR = 2.17, 95%CI = 1.2–3.8) than in female infants. Finally, the highest prevalence was recorded during winter seasons in all countries, except for Pakistan. RSV prevalence in the MENA region is comparable with the global one (24.4% vs. 22%). This first comprehensive report about RSV prevalence in the MENA region and our data should be important to guide vaccine introduction decisions and future evaluation.
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Disease severity of respiratory syncytial virus (RSV) infection correlate to a novel set of five amino acid substitutions in the RSV attachment glycoprotein (G) in China. Virus Res 2020; 281:197937. [PMID: 32194139 DOI: 10.1016/j.virusres.2020.197937] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/12/2020] [Accepted: 03/13/2020] [Indexed: 11/23/2022]
Abstract
Human respiratory syncytial virus (RSV) is one of the major viruses of acute respiratory tract disease among infants and young children. We performed molecular epidemiology analysis of RSV among inpatient children in Guangzhou, China. Phylogenetic and Bayesian analysis showed that genotype ON1 was the only subgroup A virus in this study. Interestingly, the majority of Guangzhou ON1 strains formed a well-supported cluster, and these strains shared a novel set of five amino acid substitutions that never illustrated before. Furthermore, the degree of disease severity was assessed using a severity scoring system. The patients carrying the novel RSV A strain were associated with milder respiratory symptoms compared to other RSV A positives. In conclusion, a specific set of five amino acid substitutions was found in China and further analysis showed that disease severity was associated with these alterations. These findings will provide valuable information for the pathogenic mechanism and vaccine development of RSV.
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Isolation and Characterization of Clinical RSV Isolates in Belgium during the Winters of 2016-2018. Viruses 2019; 11:v11111031. [PMID: 31698728 PMCID: PMC6893609 DOI: 10.3390/v11111031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) is a very important viral pathogen in children, immunocompromised and cardiopulmonary diseased patients and the elderly. Most of the published research with RSV was performed on RSV Long and RSV A2, isolated in 1956 and 1961, yet recent RSV isolates differ from these prototype strains. Additionally, these viruses have been serially passaged in cell culture, which may result in adaptations that affect virus–host interactions. We have isolated RSV from mucosal secretions of 12 patients in the winters 2016–2017 and 2017–2018, of which eight RSV-A subtypes and four RSV-B subtypes. Passage 3 of the isolates was assessed for viral replication kinetics and infectious virus production in HEp-2, A549 and BEAS-2B cells, thermal stability at 37 °C, 32 °C and 4 °C, syncytia formation, neutralization by palivizumab and mucin mRNA expression in infected A549 cells. We observed that viruses isolated in one RSV season show differences on the tested assays. Furthermore, comparison with RSV A2 and RSV B1 reveals for some RSV isolates differences in viral replication kinetics, thermal stability and fusion capacity. Major differences are, however, not observed and differences between the recent isolates and reference strains is, overall, similar to the observed variation in between the recent isolates. One clinical isolate (BE/ANT-A11/17) replicated very efficiently in all cell lines, and remarkably, even better than RSV A2 in the HEp-2 cell line.
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Luo HJ, Huang XB, Zhong HL, Ye CX, Tan X, Zhou K, Yuan L, Zhang SF, Zhu X, Lin CJ, Wang WJ, Xu L, Cao KY. Epidemiological characteristics and phylogenic analysis of human respiratory syncytial virus in patients with respiratory infections during 2011-2016 in southern China. Int J Infect Dis 2019; 90:5-17. [PMID: 31634614 PMCID: PMC7110755 DOI: 10.1016/j.ijid.2019.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/06/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022] Open
Abstract
For respiratory syncytial virus (RSV), an annual distribution pattern of 2-year RSV-A dominance followed by a 1-year RSV-B dominance was found in Guangzhou. In 2011–2016 in south China, prevalent RSV-A genotypes were NA1 and ON1 and the prevalent RSV-B genotype was BA9. The prevalent RSV-A genotype changed from Chongqing NA1 in 2011 to Hong Kong ON1 in 2014. The highest RSV epidemic peak occurred in 2015, indicating a possible biennial peak. The ongoing evolution of RSV-A ON1 and NA1 genotypes indicated high selection pressure.
Background Human respiratory syncytial virus (RSV) is one of the most important pathogens that cause acute respiratory infections in children and immunocompromised adults. This work was conducted to understand the epidemiological and phylogenetic features of RSV in southern China during 2011–2016. Methods A total of 16 024 nasopharyngeal swabs were collected from patients with respiratory infections in 14 hospitals, and screened for RSV and seven other respiratory viruses using real-time PCR. Six hundred and twenty-three RSV-positive samples from 13 hospitals were further analyzed for subtypes. G gene sequencing and phylogenetic analysis were performed based on 46 RSV-A and 15 RSV-B strains. Results RSV was detected in 9.5% of the 16 024 specimens, the highest among the eight respiratory viruses screened. Most of these specimens came from inpatients and children under 3 years of age. The incidence of RSV-A (9.4%) was higher than that of RSV-B (4.4%) in children (<15 years), but not in adults (0.64% vs. 0.58%). A 2-year RSV-A dominance followed by a 1-year RSV-B dominance pattern was found. The co-detection rate of RSV was 25.1%. The main prevalent genotypes were NA1, ON1, and BA9. The prevalent RSV-A genotype in 2011–2012 was NA1, close to Chongqing and Brazil, but a new Hong Kong ON1 genotype was introduced and became the prevalent genotype in Guangzhou in 2014–2015. Deduced amino acid sequence analysis confirmed the ongoing evolution and a high selection pressure of RSV-A and B strains, especially in RSV-A ON1 and NA1 genotypes. Conclusions This study demonstrated the molecular epidemiological characteristics of RSV in patients with respiratory infections in southern China.
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Affiliation(s)
- Hong-Jiao Luo
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Xu-Bin Huang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hui-Ling Zhong
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Cong-Xiu Ye
- Department of Dermatovenereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Xin Tan
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Kai Zhou
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Lei Yuan
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Su-Fen Zhang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Xun Zhu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Cui-Ji Lin
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Wen-Jun Wang
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Lin Xu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Kai-Yuan Cao
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China; Sun Yat-sen University - University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, 510080, China.
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Obodai E, Odoom JK, Adiku T, Goka B, Wolff T, Biere B, Schweiger B, Reiche J. The significance of human respiratory syncytial virus (HRSV) in children from Ghana with acute lower respiratory tract infection: A molecular epidemiological analysis, 2006 and 2013-2014. PLoS One 2018; 13:e0203788. [PMID: 30199549 PMCID: PMC6130863 DOI: 10.1371/journal.pone.0203788] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Background Acute lower respiratory tract infection (ALRI) is a leading cause of childhood morbidity and mortality in developing countries. Globally, human respiratory syncytial virus (HRSV) is the most common pathogen of ALRI in infants and children. However, age-stratified HRSV disease burden data are largely absent from Africa, which is a key gap in informing an evidence-based recommendation for the introduction of an HRSV vaccine by the WHO. Methods This study investigated the presence of HRSV in respiratory specimens from 552 children <5 years old with ALRI from Accra, Ghana in 2006 and 2013–2014 by real-time PCR. Of HRSV-positive samples the second hypervariable region of the viral G protein gene was sequenced and analyzed for phylogeny, characteristic amino acid substitutions, and potential glycosylation patterns. Further, HRSV infections have been characterized by age, symptoms and timely occurrence. Results HRSV was observed in 23% (127/552) of the children with ALRI, with the highest incidence in infants younger than one year (33%, 97/295, p = 0.013). Within the observed seasonal circulation time of HRSV from June (mid-wet season) to December (beginning of the dry season) the incidence of ALRI due to HRSV was as high as 46% (125/273). HRSV disease was significantly associated with (broncho-) pneumonia, bronchiolitis, LRTI, and difficulty in breathing. Phylogenetic characterization of HRSV strains from Ghana identified the circulation of the currently worldwide prevailing genotypes ON1 and BA9, and shows evidence of an independent molecular evolution of ON1 and BA9 strains in Ghana resulting in potentially new subgenotypes within ON1 and BA9, provisionally named ON1.5, ON1.6, and BA9-IV. Conclusion This study addresses important knowledge gaps in the forefront of introducing the HRSV vaccine by providing information on the molecular evolution and incidence of HRSV in Accra (Ghana, Africa).
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Affiliation(s)
- Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
| | - John Kofi Odoom
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Theophilus Adiku
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
| | - Bamenla Goka
- Department of Child Health, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Thorsten Wolff
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Barbara Biere
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Brunhilde Schweiger
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Janine Reiche
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
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Madi N, Chehadeh W, Asadzadeh M, Al-Turab M, Al-Adwani A. Analysis of genetic variability of respiratory syncytial virus groups A and B in Kuwait. Arch Virol 2018; 163:2405-2413. [PMID: 29777370 PMCID: PMC7087269 DOI: 10.1007/s00705-018-3881-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/07/2018] [Indexed: 01/22/2023]
Abstract
Respiratory syncytial virus (RSV) is the most frequently identified viral agent in infants, children, and elderly people with acute respiratory tract infections (ARTIs). This study is the only one of its kind in Kuwait, and its purpose was to investigate the genetic variability of the G protein gene in RSV strains prevalent in Kuwait. Respiratory samples were collected from patients with ARTIs in various hospitals in Kuwait and subjected to reverse transcription PCR (RT-PCR) amplifying a fragment of the G gene of RSV. A total of 305 samples were collected between January and mid-December 2016, and 77 (25.2%) were positive for RSV. Group A viruses were predominant over group B viruses; the RSV-A group was detected in 52 (67.5%) of the positive samples, while the RSV-B group was detected in 25 (32.5%) of the positive samples. Phylogenetic analysis showed that all RSV-A strains grouped into eight clusters of identical sequences of untyped strains. Twelve RSV-B strains, on the other hand, belonged to the RSV-B/BA10 genotype, while the rest were untyped. These data suggest that new and untyped strains of RSV-A group likely predominated in Kuwait and that the BA10 genotype of the RSV-B group became the dominant genotype in the 2016 season.
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Affiliation(s)
- Nada Madi
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait.
| | - Wassim Chehadeh
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
| | - Mohammed Asadzadeh
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
| | - Mariam Al-Turab
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
| | - Anfal Al-Adwani
- Virology Unit, Microbiology Department, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat, 13110, Kuwait City, Kuwait
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16
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Kenmoe S, Vernet MA, Miszczak F, Dina J, Schoenhals M, Beng VP, Vabret A, Njouom R. Genetic diversity of human respiratory syncytial virus isolated among children with acute respiratory infections in Southern Cameroon during three consecutive epidemic seasons, 2011-2013. Trop Med Health 2018; 46:7. [PMID: 29618942 PMCID: PMC5881174 DOI: 10.1186/s41182-018-0088-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/20/2018] [Indexed: 02/07/2023] Open
Abstract
Background Human respiratory syncytial virus (HRSV) is the main viral cause of severe lower respiratory tract disease in infants and young children. The aim of this study was to describe for the first time the genetic variability of HRSV in Cameroonian patients living in Yaounde for three consecutive epidemic seasons. Methods HRSV-positive nasopharyngeal samples detected in children less than 15 years in Yaounde were collected from September 2011 to December 2013. Semi-nested RT-PCR, sequencing, and phylogenetic analyses of the second hypervariable region of the G gene were performed. Results A total of 57 HRSV-positive samples were collected during the study period. Among these, 46 (80.7%) could be amplified in the G gene. HRSV group A (HRSV-A) and group B (HRSV-B) co-circulated in this population at 17.4 and 82.6%, respectively. HRSV-A strains clustered in the NA-1 genotype while HRSV-B strains clustered in the BA-9 genotype. HRSV-A strains accounted for 33.3% (2/6), 4.3% (1/23), and 29.4% (5/17) of the viruses isolated in 2011, 2012, and 2013, respectively. Conclusions This study reports molecular epidemiology data of HRSV in Cameroon for the first time. Additional studies are required to clarify evolutionary patterns of HRSV throughout sub-Saharan Africa to support antiviral and vaccine development.
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Affiliation(s)
- Sebastien Kenmoe
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon.,2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France.,5Département de Biochimie, Université de Yaoundé I, BP 812 Yaoundé, Cameroon
| | - Marie-Astrid Vernet
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon
| | - Fabien Miszczak
- 2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France
| | - Julia Dina
- 2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France
| | - Matthieu Schoenhals
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon
| | | | - Astrid Vabret
- 2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France
| | - Richard Njouom
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon
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17
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Abdel-Moneim AS, Soliman MS, Kamel MM, El-Kholy AA. Sequence analysis of the G gene of hRSVA ON1 genotype from Egyptian children with acute respiratory tract infections. J Med Microbiol 2018; 67:387-391. [PMID: 29458556 DOI: 10.1099/jmm.0.000699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human respiratory syncytial virus causes severe lower respiratory tract infection in neonates and children. Genotype ON1, with duplication of 72-nt in the G gene, was first detected in Canada and then recorded in other countries. In the current study, we describe the first detection of the ON1 genotype among children in Egypt in 2014/2015. Sequence analysis of the full-attachment G gene revealed that the majority of the strains examined were related to the ON1 genotype and only one sample related to N1 genotype. The Egyptian ON1 strains showed unique non-silent mutations in addition to variable mutations near the antigenic sites in comparison to the original ON1 ancestor strain. Continuous surveillance of hRSV regionally and globally is needed to understand the evolutionary mechanisms and strategies adopted by hRSV and their inducers for better adaption to the host.
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Affiliation(s)
- Ahmed S Abdel-Moneim
- Microbiology Department, College of Medicine, Taif University, Al-Taif 21944, Saudi Arabia.,Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt
| | - May S Soliman
- Clinical Pathology Department, College of Medicine, Cairo University, Giza, Egypt
| | - Mahmoud M Kamel
- Clinical Pathology Department, National Cancer Institute, Cairo University, Giza, Egypt
| | - Amani A El-Kholy
- Clinical Pathology Department, College of Medicine, Cairo University, Giza, Egypt
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18
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Hibino A, Saito R, Taniguchi K, Zaraket H, Shobugawa Y, Matsui T, Suzuki H. Molecular epidemiology of human respiratory syncytial virus among children in Japan during three seasons and hospitalization risk of genotype ON1. PLoS One 2018; 13:e0192085. [PMID: 29377949 PMCID: PMC5788364 DOI: 10.1371/journal.pone.0192085] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/16/2018] [Indexed: 12/25/2022] Open
Abstract
We investigated the genetic diversity, the circulation patterns, and risk for hospital admission of human respiratory syncytial virus (HRSV) strains in Japan between 2012 through 2015. During the study period, 744 HRSV-positive cases were identified by rapid diagnostic test. Of these, 572 samples were positive by real-time PCR; 400 (69.9%) were HRSV-A, and 172 (30.1%) were HRSV-B. HRSV-A and -B alternated as the dominant strain in the subsequent seasons. Phylogenetic tree analysis of the second hyper-variable region of the G protein classified the HRSV-A specimens into NA1 (n = 242) and ON1 (n = 114) genotypes and the HRSV-B specimens into BA9 (n = 60), and BA10 (n = 27). The ON1 genotype, containing a 72-nucleotide duplication in the G protein’s second hyper-variable region, was first detected in the 2012–2013 season but it predominated and replaced the older NA1 HRSV-A in the 2014–2015 season, which also coincided with a record number of HRSV cases reported to the National Infectious Disease Surveillance in Japan. The risk of hospitalization was 6.9 times higher for the ON1 genotype compared to NA1. In conclusion, our data showed that the emergence and predominance of the relatively new ON1 genotype in Japan was associated with a record high number of cases and increased risk for hospitalization.
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Affiliation(s)
- Akinobu Hibino
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- * E-mail:
| | | | - Hassan Zaraket
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Pathology, Immunology, and Microbiology, Faculty of Medicine American University of Beirut, Beirut, Lebanon
- Center for Infectious Disease Research, Faculty of Medicine American University of Beirut, Beirut, Lebanon
| | - Yugo Shobugawa
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tamano Matsui
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Suzuki
- School of Nursing, Niigata Seiryo University, Niigata, Japan
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Bayrakdar F, Kocabas CN, Altas AB, Kavuncuoglu HG, Cosgun Y, Mısırlıoglu ED, Durmaz I, Korukluoglu G, Ozkul A. Genetic variability human respiratory syncytial virus subgroups A and B in Turkey during six successive epidemic seasons, 2009-2015. J Med Virol 2017; 90:456-463. [PMID: 29077212 PMCID: PMC7166824 DOI: 10.1002/jmv.24983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/12/2017] [Indexed: 01/10/2023]
Abstract
Human respiratory syncytial virus (HRSV) is most important viral respiratory pathogen of acute lower respiratory tract infections in infants and young children worldwide. The circulating pattern and genetic characteristics in the HRSV attachment glycoprotein gene were investigated in Turkey during six consecutive seasons from 2009 to 2015. HRSVA was dominant in the all epidemic seasons except 2011‐2012 season. Partial sequences of the HVR2 region of the G gene of 479 HRSVA and 135 HRSVB were obtained. Most Turkish strains belonged to NA1, ON1, and BA9, which were the predominant genotypes circulating worldwide. Although three novel genotypes, TR‐A, TR‐BA1, and TR‐BA2, were identified, they were not predominant. Clinical data were available for 69 HRSV‐positive patients who were monitored due to acute lower respiratory tract illness. There were no significant differences in the clinical diagnosis, hospitalization rates, laboratory findings and treatment observed between the HRSVA and HRSVB groups, and co‐infections in this study. The major population afflicted by HRSV infections included infants and children between 13 and 24 months of age. We detected that the CB1, GB5, and THB strains clustered in the same branch with a bootstrap value of 100%. CB‐B and BA12 strains clustered in the same branch with a bootstrap value of 65%. The BA11 genotype was clustered in the BA9 genotype in our study. The present study may contribute on the molecular epidemiology of HRSV in Turkey and provide data for HRSV strains circulating in local communities and other regions worldwide.
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Affiliation(s)
- Fatma Bayrakdar
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Can Naci Kocabas
- Pediatric Immunology and Allergy Unit, Faculty of Medicine, Mugla Sitki Koçman Universty, Muğla, Turkey
| | - Ayse Basak Altas
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - H Gokhan Kavuncuoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Yasemin Cosgun
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Emine Dibek Mısırlıoglu
- Department of Pediatric Allergy and Immunology, Ankara Children's Hematology Oncology Training and Research Hospital, Ankara, Turkey
| | - Ihsan Durmaz
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Aykut Ozkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey
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20
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Song J, Wang H, Shi J, Cui A, Huang Y, Sun L, Xiang X, Ma C, Yu P, Yang Z, Li Q, Ng TI, Zhang Y, Zhang R, Xu W. Emergence of BA9 genotype of human respiratory syncytial virus subgroup B in China from 2006 to 2014. Sci Rep 2017; 7:16765. [PMID: 29196726 PMCID: PMC5711796 DOI: 10.1038/s41598-017-17055-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/21/2017] [Indexed: 01/10/2023] Open
Abstract
A study was conducted to investigate the circulation of HRSV subgroup B (HRSVB) in China in recent years. HRSVB sequences from 365 samples collected in 1991, 2004 and 2008-2014 in China, together with 332 Chinese HRSVB sequences obtained from GenBank were analyzed to determine the geographic and yearly distribution of HRSVB. Phylogenetic analysis revealed these HRSVB sequences clustered into 4 genotypes with different frequencies: BA (83%), CB1 (11%), SAB (3.0%) and GB3 (0.7%). Between 2005 and 2013, there was a co-circulation of BA and non-BA genotypes in China. Genotypes BA9 and BA10 were two of the main BA genotypes detected in this study. Genotype BA9 was first detected in China in 2006 and became the predominant HRSVB genotype circulating in China from 2008 to 2014. Three different lineages were detected for both genotypes BA9 and BA10. Time to the most recent common ancestor for genotypes BA9 and BA10 was estimated for years 1997 and 1996, respectively. Results of this study not only contribute to the understanding of the circulation pattern, but also the phylogenetic pattern and evolution of HRSVB in China from 1991 to 2014.
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Affiliation(s)
- Jinhua Song
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, 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, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jing Shi
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China.,Lu Juan Community Health Center of Daxing region, Beijing, People's Republic of China
| | - Aili Cui
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, 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
| | - Xingyu Xiang
- Hunan Provincial Centers for Disease Control and Prevention, Changsha, People's Republic of China
| | - Chaofeng Ma
- Xian Center for Disease Control and Prevention, Xian, People's Republic of China
| | - Pengbo Yu
- Shaanxi Provincial Centers for Disease Control and Prevention, Xian, 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, People's Republic of China
| | - Qi Li
- Hebei Provincial Centers for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | | | - Yan Zhang
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China.
| | - Rongbo Zhang
- Medical College, Anhui University of Science & Technology, Huainan, People's Republic of China.
| | - Wenbo Xu
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China. .,Medical College, Anhui University of Science & Technology, Huainan, People's Republic of China.
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21
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Preclinical Characterization of PC786, an Inhaled Small-Molecule Respiratory Syncytial Virus L Protein Polymerase Inhibitor. Antimicrob Agents Chemother 2017; 61:AAC.00737-17. [PMID: 28652242 PMCID: PMC5571287 DOI: 10.1128/aac.00737-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Although respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in infants and young children, attempts to develop an effective therapy have so far proved unsuccessful. Here we report the preclinical profiles of PC786, a potent nonnucleoside RSV L protein polymerase inhibitor, designed for inhalation treatment of RSV infection. PC786 demonstrated a potent and selective antiviral activity against laboratory-adapted or clinical isolates of RSV-A (50% inhibitory concentration [IC50], <0.09 to 0.71 nM) and RSV-B (IC50, 1.3 to 50.6 nM), which were determined by inhibition of cytopathic effects in HEp-2 cells without causing detectable cytotoxicity. The underlying inhibition of virus replication was confirmed by PCR analysis. The effects of PC786 were largely unaffected by the multiplicity of infection (MOI) and were retained in the face of established RSV replication in a time-of-addition study. Persistent anti-RSV effects of PC786 were also demonstrated in human bronchial epithelial cells. In vivo intranasal once daily dosing with PC786 was able to reduce the virus load to undetectable levels in lung homogenates from RSV-infected mice and cotton rats. Treatment with escalating concentrations identified a dominant mutation in the L protein (Y1631H) in vitro. In addition, PC786 potently inhibited RSV RNA-dependent RNA polymerase (RdRp) activity in a cell-free enzyme assay and minigenome assay in HEp-2 cells (IC50, 2.1 and 0.5 nM, respectively). Thus, PC786 was shown to be a potent anti-RSV agent via inhibition of RdRp activity, making topical treatment with this compound a novel potential therapy for the treatment of human RSV infections.
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22
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Emergence of ON1 genotype of human respiratory syncytial virus subgroup A in China between 2011 and 2015. Sci Rep 2017; 7:5501. [PMID: 28710393 PMCID: PMC5511225 DOI: 10.1038/s41598-017-04824-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/22/2017] [Indexed: 11/23/2022] Open
Abstract
A molecular epidemiological study of human respiratory syncytial virus (HRSV) was conducted to examine the distribution of its subgroups and genotypes, as well as to identify its transmission pattern in China. A total of 705 samples collected from 9 provinces in China between January 2008 and February 2015 were identified as HRSV-positive and were subsequently sequenced. Of these, 336 samples were HRSV subgroup A (HRSVA), 368 samples were HRSV subgroup B (HRSVB), and 1 sample contained both HRSVA and HRSVB. These 705 HRSV sequences, together with 766 HRSV sequences downloaded from GenBank, were analyzed to understand the recent circulation patterns of HRSV in China. HRSVB predominated in the 2008/2009 and 2009/2010 seasons, whereas HRSVA predominated in the 2010/2011 and 2011/2012 seasons; HRSVA and HRSVB co-circulated during 2012/2013 and 2014/2015. Phylogenetic analysis showed most of the HRSVA sequences clustered into 2 genotypes, namely, NA1 and ON1. The ON1 genotype was first detected in China in 2011, and it quickly replaced the NA1 genotype to become the most prevalent HRSVA genotype circulating in China between 2013 and 2015. Continuous epidemiological surveillance and molecular characterization of HRSV should be conducted to monitor the evolution of HRSV in China.
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23
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Ábrego LE, Delfraro A, Franco D, Castillo J, Castillo M, Moreno B, López-Vergès S, Pascale JM, Arbiza J. Genetic variability of human respiratory syncytial virus group B in Panama reveals a novel genotype BA14. J Med Virol 2017; 89:1734-1742. [PMID: 28464479 DOI: 10.1002/jmv.24838] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/24/2017] [Accepted: 04/17/2017] [Indexed: 11/10/2022]
Abstract
In Panama, human respiratory syncytial virus (HRSV) is responsible of 20-40% of acute respiratory infections in children under 5 years old. Currently, little is known about the genetic variability of HRSV in Central America and the Caribbean. Recently, we reported the genetic variability of HRSV-A, however; no studies on HRSV-B in Panama have been described yet. In this study, 24 sequences of Panamanian HRSV-B, from children (<5 years) with acute respiratory infections (ARI), collected from July 2008 to November 2012 were analyzed. All sequences share the characteristic 60-nt duplication of the BA strains. Six Panamanian strains grouped with the BA10 genotype and 12 samples clustered together in a separate monophyletic clade with an aLRT support value of 0.92 and an intra-group p-distance less than 0.07. This fulfills the criteria to consider a new genotype in HRSV, which we named BA14 genotype. Another six strains remain unclassified, but closely related to BA9, BA11, or the new BA14 genotypes, according to their genetic p-distance. Different amino acid substitutions in the Panamanian HRSV-B strains were observed, some previously described and others found only on Panamanian strains. This study contributes to the knowledge of the genetic variability and evolution of HRSV in Central America.
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Affiliation(s)
- Leyda E Ábrego
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Adriana Delfraro
- Virology Section, School of Sciences, University of the Republic, Montevideo, Uruguay
| | - Danilo Franco
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama.,School of Medicine, University of Panama, Panama City, Panama
| | - Juan Castillo
- Department of Genomic and Proteomic, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Marlene Castillo
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Brechla Moreno
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Sandra López-Vergès
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Juan M Pascale
- School of Medicine, University of Panama, Panama City, Panama.,Department of Genomic and Proteomic, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Juan Arbiza
- Virology Section, School of Sciences, University of the Republic, Montevideo, Uruguay
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24
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Kimura H, Nagasawa K, Kimura R, Tsukagoshi H, Matsushima Y, Fujita K, Hirano E, Ishiwada N, Misaki T, Oishi K, Kuroda M, Ryo A. Molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B. INFECTION GENETICS AND EVOLUTION 2017; 52:1-9. [PMID: 28414106 DOI: 10.1016/j.meegid.2017.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/09/2017] [Accepted: 04/12/2017] [Indexed: 11/19/2022]
Abstract
In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes. The MCMC-constructed phylogenetic tree indicated that the HRSV F gene diverged from the bovine respiratory syncytial virus gene approximately 580years ago and had a relatively low evolutionary rate (7.14×10-4substitutions/site/year). Furthermore, a common ancestor of HRSV-A and -B diverged approximately 290years ago, while HRSV-B diverged into three clusters for approximately 60years. The genetic similarity of the present strains was very high. Although a maximum of 11 amino acid substitutions were observed in the structural model of the F protein, only one strain possessed an amino acid substitution located within the palivizumab epitope. Four epitopes were predicted, although these did not correspond to the neutralization sites of the F protein including the palivizumab epitope. In addition, five N-glycosylation sites of the present HRSV-B strains were inferred. No positive selection sites were identified; however, many sites were found to be under negative selection. The effective population size of the gene has remained almost constant. On the basis of these results, it can be concluded that the HRSV-B F gene is highly conserved, as is the F protein of HRSV-A. Moreover, our prediction of B-cell epitopes does not show that the palivizumab reaction site may be recognized as an epitope during naturally occurring infections.
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Affiliation(s)
- Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Ryusuke Kimura
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 37-1 Nakaoruimachi, Takasaki-shi, Gunma 370-0033, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Yuki Matsushima
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kiyotaka Fujita
- School of Medical Technology, Faculty of Health Science, Gumma Paz College, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, 39-4 Harame-cho, Fukui-shi, Fukui 910-8851, Japan
| | - Naruhiko Ishiwada
- Division of Infection Control and Prevention, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan
| | - Takako Misaki
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
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25
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Fan R, Fan C, Zhang J, Wen B, Lei Y, Liu C, Chen L, Liu W, Wang C, Qu X. Respiratory syncytial virus subtype ON1/NA1/BA9 predominates in hospitalized children with lower respiratory tract infections. J Med Virol 2016; 89:213-221. [PMID: 27358012 PMCID: PMC7166484 DOI: 10.1002/jmv.24619] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 12/02/2022]
Abstract
Respiratory syncytial virus (RSV) infection is the leading cause of acute respiratory tract disease in children less than 5 years old. The aim of this study was to further elucidate the molecular properties and clinical characteristics of RSV infection. The study sample included 238 patients <5 years old who were hospitalized with clinical symptoms of upper or lower respiratory tract infection (URTI or LRTI) in the Pediatric Department at the First People's Hospital of Chenzhou, South China in 2014. We subjected nasopharyngeal aspirate (NPA) or nasal swab (NS) samples from the patients to indirect fluorescence assay screens. RSV G genes were amplified by reverse transcription‐PCR (RT‐PCR) and sequenced. Of the 238 patients screened, 64 (26.8%) were confirmed to have RSV infections. Of those 64 confirmed RSV infection cases, 39 (60.9%) had subtype BA9, 13 (20.3%) had the recently identified subtype ON1, 11 (17.2%) had subtype NA1, and 1 (1.6%) had subtype GB2. The predominant presentation was LRTI with coughing, sputum production, fever, and wheezing. RSV subtype NA1 and BA9 infections were found mostly in infants, whereas the age distribution of subtype ON1 infections was more uniform across the age bands. Phylogenetic analysis indicated that, compared with the prototype strain A2, all ON1 and most NA1 isolates had lost one potential N‐glycosylation site at amino acid 251 and 249 due to T251K and N249Y substitution, respectively. These findings suggest that NA1, BA9, and ON1 are the dominant RSV subtypes causing respiratory tract infections in young children presenting to the hospital in South China. J. Med. Virol. 89:213–221, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ruyan Fan
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China.,Department of Pediatric, Guangzhou Women and Children's Medical Center, Guangzhou, People's Republic of China
| | - Chuping Fan
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Jian Zhang
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Bo Wen
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Yefei Lei
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Chan Liu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Lijuan Chen
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Wenpei Liu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Chuan Wang
- Department of Public Health, Sichuan University, Chengdu, People's Republic of China
| | - Xiaowang Qu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
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26
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Hu P, Zheng T, Chen J, Zhou T, Chen Y, Xu X, Pei X. Alternate circulation and genetic variation of human respiratory syncytial virus genotypes in Chengdu, West China, 2009-2014. J Med Virol 2016; 89:32-40. [PMID: 27322084 DOI: 10.1002/jmv.24603] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2016] [Indexed: 11/05/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a major pathogen that causes worldwide seasonal epidemic disease in infants due to its genetic variations. However, published information on the molecular epidemiology of HRSV was never reported particularly in Chengdu of West China. During five consecutive seasons (from 2009 to 2014), 433 (23.7%) of 1827 samples from hospitalized patients were identified as HRSV positive. Epidemiological characteristics of HRSV revealed that subtype A viruses (62.7%) prevailed in the first three epidemic seasons and faded in the next two seasons, while subtype B viruses (37.3%) kept circulating in five epidemic periods. According to the phylogenetic analysis of glycoprotein (G) gene, five HRSV genotypes NA1, ON1, BA9, BA-C, and CB1 were found in Chengdu. The predominant circulating genotype changed from NA1 in the period of 2010-2012 to BA9 of 2013-2014. The newly emerging ON1 was first reported in West China in October 2013. The early genotypes BA-C and CB1 were replaced by the prevailing BA9 after the third epidemic peak. Genetic mutations in glycosylation sites of G protein were found in HRSV variants, suggesting the virus is able to escape the immune recognition and attack. This study elucidated the local HRSV epidemic was associated with the alternate circulation of multiple genotypes and with the change of glycosylation sites of G protein. J. Med. Virol. 89:32-40, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Pengwei Hu
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China.,Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Tianli Zheng
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Jiayi Chen
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Tao Zhou
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Yuhang Chen
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xin Xu
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xiaofang Pei
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China.
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27
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Malasao R, Okamoto M, Chaimongkol N, Imamura T, Tohma K, Dapat I, Dapat C, Suzuki A, Saito M, Saito M, Tamaki R, Pedrera-Rico GAG, Aniceto R, Quicho RFN, Segubre-Mercado E, Lupisan S, Oshitani H. Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012-2013. PLoS One 2015; 10:e0142192. [PMID: 26540236 PMCID: PMC4635013 DOI: 10.1371/journal.pone.0142192] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/19/2015] [Indexed: 12/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of acute lower respiratory tract infections in infants and children worldwide. We performed molecular analysis of HRSV among infants and children with clinical diagnosis of severe pneumonia in four study sites in the Philippines, including Biliran, Leyte, Palawan, and Metro Manila from June 2012 to July 2013. Nasopharyngeal swabs were collected and screened for HRSV using real-time polymerase chain reaction (PCR). Positive samples were tested by conventional PCR and sequenced for the second hypervariable region (2nd HVR) of the G gene. Among a total of 1,505 samples, 423 samples were positive for HRSV (28.1%), of which 305 (72.1%) and 118 (27.9%) were identified as HRSV-A and HRSV-B, respectively. Two genotypes of HRSV-A, NA1 and ON1, were identified during the study period. The novel ON1 genotype with a 72-nucleotide duplication in 2nd HVR of the G gene increased rapidly and finally became the predominant genotype in 2013 with an evolutionary rate higher than the NA1 genotype. Moreover, in the ON1 genotype, we found positive selection at amino acid position 274 (p<0.05) and massive O- and N-glycosylation in the 2nd HVR of the G gene. Among HRSV-B, BA9 was the predominant genotype circulating in the Philippines. However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains. These findings suggest that HRSV is an important cause of severe acute respiratory infection among children in the Philippines and revealed the emergence and subsequent predominance of the ON1 genotype and the sporadic detection of the GB2 genotype. Both genotypes were detected for the first time in the Philippines.
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Affiliation(s)
| | - Michiko Okamoto
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | | | - Kentaro Tohma
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Isolde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Clyde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Suzuki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayuko Saito
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | - Raita Tamaki
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | | | - Rapunzel Aniceto
- Eastern Visayas Regional Medical Center, Tacloban City, Philippines
| | | | | | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
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28
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Zhou L, Xiao Q, Zhao Y, Huang A, Ren L, Liu E. The impact of viral dynamics on the clinical severity of infants with respiratory syncytial virus bronchiolitis. J Med Virol 2015; 87:1276-84. [PMID: 25907780 PMCID: PMC7166664 DOI: 10.1002/jmv.24111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2014] [Indexed: 01/30/2023]
Abstract
The impact of dynamic respiratory syncytial virus (RSV) load on the clinical severity of hospitalized infants with bronchiolitis has not been clarified. Nasopharyngeal aspirates were obtained from 60 infants who were diagnosed with bronchiolitis within 96 hr of wheezing onset upon admission and on days 3, 5, and 7 in the hospital, and 17 respiratory viruses were detected. The RSV load was quantified by real-time qPCR for RSV subtypes A and B at different time points. Scoring criteria were used to evaluate the degree of severity. A total of 40 infants were determined to be RSV-positive, nine were identified as RSV subtype A (RSVA), and 31 were RSV subtype B (RSVB). The peak RSV load was observed upon admission, and the RSV load decreased significantly over time; in addition, this decrease began to have significant differences on day 5. There was a positive correlation between the RSV load and the clinical score (r(2) = 0.121 and P < 0.001). According to the clinical scores, the infants in the severe group tended to have higher RSV loads than those in the moderate and mild groups. Multivariate logistic regression models revealed that the viral load on day 3 was independently associated with the degree of severity. This study elucidated that a higher mean RSV load was associated with a more severe disease and a longer duration of hospitalization and symptoms. This study also clarified RSV replication in infants and provides a theoretical basis for specifying an anti-RSV therapy strategy.
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Affiliation(s)
- Lili Zhou
- Ministry of Education Key Laboratory of Child Development and DisordersChongqing International Science and Technology Cooperation Center for Child Development and DisordersChongqingChina
- Key Laboratory of Pediatrics in Chongqing CSTC2009CA5002ChongqingChina
- Department of Respiratory MedicineWomen and Children's hospitalGanzhou, JiangxiChina
| | - Qiuyan Xiao
- Ministry of Education Key Laboratory of Child Development and DisordersChongqing International Science and Technology Cooperation Center for Child Development and DisordersChongqingChina
- Key Laboratory of Pediatrics in Chongqing CSTC2009CA5002ChongqingChina
| | - Yao Zhao
- Ministry of Education Key Laboratory of Child Development and DisordersChongqing International Science and Technology Cooperation Center for Child Development and DisordersChongqingChina
- Key Laboratory of Pediatrics in Chongqing CSTC2009CA5002ChongqingChina
| | - Ailong Huang
- Key Laboratory of Molecular Biology of Infectious DiseasesMinistry of EducationChongqing Medical UniversityChongqingChina
| | - Luo Ren
- Ministry of Education Key Laboratory of Child Development and DisordersChongqing International Science and Technology Cooperation Center for Child Development and DisordersChongqingChina
- Key Laboratory of Pediatrics in Chongqing CSTC2009CA5002ChongqingChina
| | - Enmei Liu
- Department of Respiratory MedicineChildren's HospitalChongqing Medical UniversityChongqingChina
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