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Madi N, Safar HA, Al-Adwani A, Sadeq M, Al-Turab M. Genomic characterization of circulating human respiratory syncytial viruses A and B in Kuwait using whole-genome sequencing. Microbiol Spectr 2024; 12:e0015924. [PMID: 38808977 PMCID: PMC11218466 DOI: 10.1128/spectrum.00159-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
The human respiratory syncytial virus (RSV) is considered one of the most common viruses that infect children globally. The virus is known to have extensive gene sequence variability within and between RSV groups A and B globally; however, there is no information on the whole-genome characterization and diversity of RSV in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with acute respiratory tract infection (ARTI) in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with ARTI in Kuwait. Between January 2020 and September 2022, 7,093 respiratory samples were collected from hospitalized infants, children, and adults and were analyzed for respiratory viruses by multiplex real-time PCR. Whole-genome sequencing using the Oxford Nanopore sequencing technology was performed on 84 RSV-positive samples. The results revealed a higher prevalence of group A (76%) than group B (24%) RSV isolates. Phylogenetic analysis showed that RSV-A strains clustered with the GA2.3.5 sub-genotype and RSV-B strains clustered with the GB5.0.5a sub-genotype; however, forming new lineages of RSV-A and RSV-B circulated in Kuwait during this period. Genetic variability was higher among the group A viruses than group B viruses, and the rate of synonymous and missense mutations was high in genes other than the G protein-coding gene. We also detected several known and unique molecular markers in different protein-coding genes. This is the first study in Kuwait to characterize the whole genomes of RSV A and B to identify the circulating genotypes, comprehend the genetic diversity and the evolution of the virus, and identify important genetic markers associated with specific genotypes.IMPORTANCEWhole-genome sequencing of respiratory syncytial virus (RSV) strains in Kuwait using MinION Nanopore technology was used to characterize and analyze the genotypes and sub-genotypes of the RSV circulating among patients with acute respiratory tract infections in Kuwait. This study also identified known and unknown gene mutations and imported genetic markers associated with specific genotypes. These results will assist in establishing a framework for RSV classification and allow for a better consideration of the mechanisms leading to the generation of diversity of RSV. In addition, these data will allow a comparison of vaccine viruses with those in Kuwait, providing useful insights into future vaccine and therapy strategies for RSV in Kuwait.
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Affiliation(s)
- Nada Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Hussain A. Safar
- Research Core Facility and OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Anfal Al-Adwani
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Mohammed Sadeq
- Jaber Al-Ahmad Armed Forces Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Mariam Al-Turab
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
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Yang S, Lu S, Wang Y, Guo Y, Zhang Z, Wang W, Wang L. Respiratory syncytial virus subtypes in children with bronchiolitis: does it correlate with clinical severity? BMC Infect Dis 2024; 24:263. [PMID: 38408969 PMCID: PMC10898063 DOI: 10.1186/s12879-024-09129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND In this retrospective study, we aimed to evaluate the factors associated with the severity of respiratory syncytial virus (RSV) bronchiolitis in children aged under 2 years who were admitted to the Children's Hospital of Hebei between June 2018 and January 2019. METHODS Sputum samples positive for RSV via multiplex PCR were subtyped using real-time PCR. Data collected included risk factors for disease severity, demographics, microbiology, and outcomes. RESULTS Of the 82 children with RSV bronchiolitis, 79 were treated and discharged with improvement, while 3 died. All three patients had underlying medical conditions, including complex congenital heart disease and severe combined immunodeficiency. Further, disease severity was associated with preexisting underlying disease, fever duration, and bacterial co-infection, but not with the RSV subtype. CONCLUSIONS Our findings suggest that an appropriate therapeutic regimen should include the detection of bacterial co-infections and the identification of underlying diseases for the effective management of severe RSV bronchiolitis.
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Affiliation(s)
- Shuo Yang
- Institute of Pediatric Research, Children's Hospital of Hebei, 133 Jianhua South Street, 050031, Shijiazhuang, Hebei Province, China
| | - Sukun Lu
- Institute of Pediatric Research, Children's Hospital of Hebei, 133 Jianhua South Street, 050031, Shijiazhuang, Hebei Province, China
| | - Yakun Wang
- Institute of Pediatric Research, Children's Hospital of Hebei, 133 Jianhua South Street, 050031, Shijiazhuang, Hebei Province, China
| | - Yinghui Guo
- Institute of Pediatric Research, Children's Hospital of Hebei, 133 Jianhua South Street, 050031, Shijiazhuang, Hebei Province, China
| | - Zhuang Zhang
- Ningbo HEALTH Gene Technologies Co., Ltd, 315000, Ningbo, China
| | - Weijian Wang
- Ningbo HEALTH Gene Technologies Co., Ltd, 315000, Ningbo, China
| | - Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei, 133 Jianhua South Street, 050031, Shijiazhuang, Hebei Province, China.
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Umar S, Yang R, Wang X, Liu Y, Ke P, Qin S. Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China. Virol J 2023; 20:272. [PMID: 37993935 PMCID: PMC10666375 DOI: 10.1186/s12985-023-02227-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection and hospitalization, especially in children. Highly mutagenic nature and antigenic diversity enable the RSV to successfully survive in human population. We conducted a molecular epidemiological study during 2017-2021 to investigate the prevalence and genetic characteristics of RSV. METHODS A total of 6499 nasopharyngeal (NP) swabs were collected from hospitalized children at Department of Pediatrics, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong, China. All NP swab specimens were preliminary screened for common respiratory viruses and then tested for RSV using specific PCR assays. Partial G genes of RSV were amplified for phylogenetic analysis and genetic characterization. RESULTS The overall detection rate for common respiratory viruses was 16.12% (1048/6499). Among those, 405 specimens (6.20%, 405/6499) were found positive for RSV. The monthly distribution of RSV and other respiratory viruses was variable, and the highest incidence was recorded in Autumn and Winter. Based on the sequencing of hypervariable region of G gene, 93 RSV sequences were sub-grouped into RSV-A (56, 60.2%) and RSV-B (37, 39.8%). There was no coinfection of RSV-A and RSV-B in the tested samples. Phylogenetic analysis revealed that RSV-A and RSV-B strains belonged to ON1 and BA9 genotypes respectively, indicating predominance of these genotypes in Guangzhou. Several substitutions were observed which may likely change the antigenicity and pathogenicity of RSV. Multiple glycosylation sites were noticed, demonstrating high selection pressure on these genotypes. CONCLUSION This study illustrated useful information about epidemiology, genetic characteristics, and circulating genotypes of RSV in Guangzhou China. Regular monitoring of the circulating strains of RSV in different parts of China could assist in the development of more effective vaccines and preventive measures.
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Affiliation(s)
- Sajid Umar
- Global Health Research Center, Duke Kunshan University, Kunshan, China
- Division of Natural and Applied Sciences (DNAS), Duke Kunshan University, Kunshan, China
| | - Rongyuan Yang
- Key Laboratory for Infectious Disease, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinye Wang
- School of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China.
| | - Sheng Qin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China.
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Li H, Wu X, Zeng H, Chang B, Cui Y, Zhang J, Wang R, Ding T. Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections. MICROBIOME 2023; 11:157. [PMID: 37482605 PMCID: PMC10364384 DOI: 10.1186/s40168-023-01597-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Secondary bacterial infections and pneumonia are major mortality causes of respiratory viruses, and the disruption of the upper respiratory tract (URT) microbiota is a crucial component of this process. However, whether this URT dysbiosis associates with the viral species (in other words, is viral type-specific) is unclear. RESULTS Here, we recruited 735 outpatients with upper respiratory symptoms, identified the infectious virus types in 349 participants using multiplex RT-PCR, and profiled their upper respiratory microbiome using the 16S ribosomal RNA gene and metagenomic gene sequencing. Microbial and viral data were subsequently used as inputs for multivariate analysis aimed at revealing viral type-specific disruption of the upper respiratory microbiota. We found that the oropharyngeal microbiota shaped by influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (RSV), and human rhinovirus (HRV) infections exhibited three distinct patterns of dysbiosis, and Veillonella was identified as a prominent biomarker for any type of respiratory viral infections. Influenza virus infections are significantly correlated with increased oropharynx microbiota diversity and enrichment of functional metabolic pathways such as L-arginine biosynthesis and tetracycline resistance gene tetW. We used the GRiD algorithm and found the predicted growth rate of common respiratory pathogens was increased upon influenza virus infection, while commensal bacteria, such as Streptococcus infantis and Streptococcus mitis, may act as a colonization resistance to the overgrowth of these pathogens. CONCLUSIONS We found that respiratory viral infections are linked with viral type-specific disruption of the upper respiratory microbiota, particularly, influenza infections uniquely associated with increased microbial diversity and growth rates of specific pathogens in URT. These findings are essential for clarifying the differences and dynamics of respiratory microbiota in healthy participants and acute respiratory viral infections, which contribute to elucidating the pathogenesis of viral-host-bacterial interactions to provide insights into future studies on effective prevention and treatment of respiratory tract infections. Video Abstract.
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Affiliation(s)
- Hui Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Xiaorong Wu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Hong Zeng
- Center for Disease Control and Prevention of Nanhai District, Foshan, 528200, China
| | - Bozhen Chang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Jingxiang Zhang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ruixia Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
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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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ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia. Genes (Basel) 2022; 13:genes13122288. [PMID: 36553555 PMCID: PMC9778264 DOI: 10.3390/genes13122288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.
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Pre COVID-19 molecular epidemiology of respiratory syncytial virus (RSV) among children in Bangladesh. Heliyon 2022; 8:e11043. [PMID: 36247113 PMCID: PMC9551109 DOI: 10.1016/j.heliyon.2022.e11043] [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: 11/02/2021] [Revised: 02/24/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Epidemiological data of specific respiratory pathogens from the pre-COVID-19 period are essential to determine the effects of the COVID-19 pandemic on other respiratory infections. In this study, we revealed the pre-COVID-19 molecular epidemiology of respiratory syncytial virus (RSV) among children in Bangladesh. We tested 3170 samples collected from 2008 to 2012 for a panel of respiratory viruses; RSV, human metapneumovirus (hMPV), human parainfluenza viruses (hPIV) 1, 2, 3, and adenovirus. Five hundred fifty-five samples (17.5 %) were positive for RSV, including 2.5% having co-infections with other viruses. Genotypic characterization of RSV showed that RSV-A (82%) contributed more acute respiratory infections than RSV-B (18%). Clinical features were similar with RSV-A and RSV-B infections. However, children with RSV-B were more likely to have upper respiratory infections (URI) (10% vs. 29%, p = 0.03). Among RSV-A cases, hospitalization was higher for ON1 cases (25%, ON1 vs. 8%, NA1, p = 0.04), whereas the recovery without a disability was higher among the NA1 cases (56%, ON1 vs. 88%, NA1, p = 0.02). The time to the most recent common ancestor (TMRCA) for RSV in Bangladesh was 1949 for RSV-A and 1944 for RSV-B. This study revealed the genotypic diversity and evolutionary relatedness of RSV strains in Bangladesh and provided pre-COVID molecular epidemiology data to understand better the COVID-19 impact on upcoming RSV epidemiology in Bangladesh.
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Zhao X, Wang C, Jiang H, Zhang H, Fang F, Chen M, Yuan Z, Teng Z, Liu J, Zhang X. Analysis of circulating respiratory syncytial virus A strains in Shanghai, China identified a new and increasingly prevalent lineage within the dominant ON1 genotype. Front Microbiol 2022; 13:966235. [PMID: 36033866 PMCID: PMC9403419 DOI: 10.3389/fmicb.2022.966235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial virus A (RSV-A) is one of the commonest pathogens causing acute respiratory tract infections in infants and children globally. The currently dominant circulating genotype of RSV-A, ON1, was first detected in Shanghai, China in 2011, but little data are available regarding its subsequent circulation and clinical impact here. In this work, we analyzed RSV-A infection in a cohort of patients hospitalized for acute respiratory infections in Shanghai Children’s Hospital, and RSV-A was detected in ~10% of these cases. RSV-A G gene sequencing revealed that all successfully sequenced strains belonged to ON1 genotype, but in phylogenetic analysis, the majority of these sequences formed a clade separate from the four previously established lineages within ON1. The new lineage, denoted ON1-5, was supported by phylogenetic analyses using additional G gene sequences from RSV-A strains isolated in Shanghai and elsewhere. ON1-5 first appeared in 2015 in China and the Netherlands, and has since spread to multiple continents and gained dominance in Asia. In our cohort, ON1-5 was not associated with markedly different clinical presentations compared to other ON1 lineages. ON1-5 strains are characterized by four amino acid variations in the two mucin-like regions of G protein, and one variation (N178G) within the highly conserved CCD domain that is involved in receptor binding. These data highlight the continuous evolution of RSV-A, and suggest the possibility of the virus acquiring variations in domains traditionally considered to be conserved for fitness gain.
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Affiliation(s)
- Xue Zhao
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Hui Jiang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Fanghao Fang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Min Chen
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zhengan Yuan
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zheng Teng
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- *Correspondence: Zheng Teng,
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (MOE/MOH/CAMS) and Shanghai Key Laboratory of Medical Epigenetics, Department of Microbiology and Parasitology and Institutes of Biomedical Sciences, School of Basic Medical Sciences and Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, China
- Jing Liu,
| | - Xi Zhang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Xi Zhang,
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Genetic Diversity and Epidemiological Features of Respiratory Syncytial Virus, Beijing, 2015–2019: A Multicenter and All-Age Groups Study. J Infect 2022; 85:75-85. [DOI: 10.1016/j.jinf.2022.04.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/19/2022]
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Pappa S, Haidopoulou K, Zarras C, Theodorakou E, Papadimitriou E, Iosifidis E, Gkeka I, Stoikou K, Vagdatli E, Skoura L, Papa A. Early initiation of the respiratory syncytial virus season in 2021-2022, Greece. J Med Virol 2022; 94:3453-3456. [PMID: 35199347 DOI: 10.1002/jmv.27671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/04/2022] [Accepted: 02/20/2022] [Indexed: 11/11/2022]
Abstract
Respiratory syncytial virus (RSV) is the most common viral pathogen causing respiratory disease in the pediatric population. An unexpected sudden upsurge of RSV infections among children was observed in September 2021 in Greece. Forty-one rhinopharyngeal samples from children under the age of 2 years with confirmed RSV bronchiolitis were tested to identify the genotype(s) of the RSV strain(s). The children were hospitalized during September-November 2021 in three tertiary hospitals in northern Greece. A one-step RT-PCR which amplifies a fragment of the second hypervariable region of the G protein gene was applied. PCR products were sequenced, and phylogenetic analysis was performed. Most (80.5%) RSV cases were typed as RSV-A, with RSV-B accounting for 19.5% of cases. RSV-A and RSV-B sequences clustered within the ON1 and BA genotypes, respectively. Since the same genotypes were detected in cases observed during 2016-2018 in northern Greece, it was suggested that the early upsurge of infections was not related to the emergence of novel strain(s), but it was the result of the absence of immunity among children and their mothers due to the restriction measures taken during the COVID-19 pandemic in the previous RSV season. Awareness is needed to diagnose even the out-of-season RSV infections, while molecular epidemiology plays a key role in monitoring the efficacy of currently available therapeutics and for those under development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Styliani Pappa
- Laboratory of Microbiology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Katerina Haidopoulou
- 2nd Department of Pediatrics, AHEPA Hospital, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Charalampos Zarras
- Microbiology Department, Hippokration General Hospital, Thessaloniki, Greece
| | | | - Eleni Papadimitriou
- 1st Department of Pediatrics, Hippokration General Hospital, Thessaloniki, Greece
| | - Elias Iosifidis
- Infectious Disease Unit, 3rd Department of Pediatrics, School of Medicine, Hippokration General Hospital, Thessaloniki, Greece
| | - Ioanna Gkeka
- Microbiology Laboratory, AHEPA Hospital, School of Medicine, Aristotle University of Thessaloniki, Greece
| | - Konstantina Stoikou
- Laboratory of Microbiology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Vagdatli
- Microbiology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Lemonia Skoura
- Microbiology Laboratory, AHEPA Hospital, School of Medicine, Aristotle University of Thessaloniki, Greece
| | - Anna Papa
- Laboratory of Microbiology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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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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Zhao X, Meng Y, Li D, Feng Z, Huang W, Li X, Wei H, Zeng X, Wang D. Retrospective study of clinical characteristics and viral etiologies of patients with viral pneumonia in Beijing. Pulm Circ 2021; 11:20458940211011027. [PMID: 34221349 PMCID: PMC8221751 DOI: 10.1177/20458940211011027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Aims The virus is common in patients with viral pneumonia. However, the viral etiology and clinical features of patients with viral pneumonia in China remain unclear. The main purpose of this study was to analyze the viral causes and epidemiology of patients with viral pneumonia in Beijing, which can significantly improve the pertinence and accuracy of clinical treatment of the disease. Methods Firstly, 1539 respiratory specimens of pneumonia (oropharyngeal swabs, nasopharyngeal swabs, saliva samples and bronchoalveolar lavage fluid) were collected from 19 hospitals in Beijing from September 2015 to August 2018. Then, TaqMan low-density microfluidic chip technology was used to detect viral pneumonia specimens in 1539 respiratory tract specimens of pneumonia and determine the types of viral bacteria in them. Lastly, the analysis of demographic, clinical and etiological data of patients with viral pneumonia was performed. Results The results showed that among the 1539 respiratory tract specimens with pneumonia, 760 were detected as viral pneumonia specimens, with a positive rate of 49.4%. Among which, 467 were infected with mono-viral and 293 were infected with multi-viral. Influenza A virus (Flu A), mycoplasma pneumoniae (MPn), Ebola virus (EBV) and herpes simplex virus type 1 (HSV-1) were the major viral components in the samples of these patients. Furthermore, these viral species were significantly associated with sample sources, onset season and certain clinical characteristics. Discussion Our findings may provide corresponding treatment strategies for viral pneumonia patients infected with specific viruses.
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Affiliation(s)
- Xiang Zhao
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Yao Meng
- Department of Influenza, Shaanxi Provincial Center for Disease Control and Prevention, Xian City, PR China
| | - Duo Li
- Department of Influenza, Yunnan Provincial Center for Disease Control and Prevention, Kunming City, PR China
| | - Zhaomin Feng
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Weijuan Huang
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Xiyan Li
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Hejiang Wei
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Xiaoxu Zeng
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Dayan Wang
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
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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: 14] [Impact Index Per Article: 4.7] [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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Global Molecular Epidemiology of Respiratory Syncytial Virus from the 2017-2018 INFORM-RSV Study. J Clin Microbiol 2020; 59:JCM.01828-20. [PMID: 33087438 PMCID: PMC7771447 DOI: 10.1128/jcm.01828-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children, resulting in annual epidemics worldwide. INFORM-RSV is a multiyear clinical study designed to describe the global molecular epidemiology of RSV in children under 5 years of age by monitoring temporal and geographical evolution of current circulating RSV strains, F protein antigenic sites, and their relationships with clinical features of RSV disease. During the pilot season (2017–2018), 410 RSV G-F gene sequences were obtained from 476 RSV-positive nasal samples collected from 8 countries (United Kingdom, Spain, The Netherlands, Finland, Japan, Brazil, South Africa, and Australia). Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children, resulting in annual epidemics worldwide. INFORM-RSV is a multiyear clinical study designed to describe the global molecular epidemiology of RSV in children under 5 years of age by monitoring temporal and geographical evolution of current circulating RSV strains, F protein antigenic sites, and their relationships with clinical features of RSV disease. During the pilot season (2017–2018), 410 RSV G-F gene sequences were obtained from 476 RSV-positive nasal samples collected from 8 countries (United Kingdom, Spain, The Netherlands, Finland, Japan, Brazil, South Africa, and Australia). RSV B (all BA9 genotype) predominated over RSV A (all ON1 genotype) globally (69.0% versus 31.0%) and in all countries except South Africa. Geographic clustering patterns highlighted wide transmission and continued evolution with viral spread. Most RSV strains were from infants of <1 year of age (81.2%), males (56.3%), and patients hospitalized for >24 h (70.5%), with no differences in subtype distribution. Compared to 2013 reference sequences, variations at F protein antigenic sites were observed for both RSV A and B strains, with high-frequency polymorphisms at antigenic site Ø (I206M/Q209R) and site V (L172Q/S173L/K191R) in RSV B strains. The INFORM-RSV 2017–2018 pilot season establishes an important molecular baseline of RSV strain distribution and sequence variability with which to track the emergence of new strains and provide an early warning system of neutralization escape variants that may impact transmission or the effectiveness of vaccines and MAbs under development.
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Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia. Genes (Basel) 2020; 11:genes11111323. [PMID: 33182267 PMCID: PMC7695323 DOI: 10.3390/genes11111323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial virus (HRSV) is a main cause of hospital admission for lower respiratory tract infection. In previous studies from Saudi Arabia, higher prevalence of the NA1 genotype in group A was observed from Riyadh and Taif. This study recruited respiratory cases from Jeddah during January to December, 2017. RSV represented 13.4% in the recruited cases with 64% of them belonging to group A and 36% to group B. All group A cases in this study were ON1 type characterized by duplication of 72 nucleotides, 24 amino acids in the C-terminal in the second hypervariable region of the G gene. In addition, for group B all of the cases were clustered under BA9, which had uniquely characterized as duplication of 60 nucleotides in the G protein. Our sequences showed similarity with earlier sequences from Saudi Arabia, Kuwait, Thailand, South Africa, Spain, the USA and Cyprus. Some amino acid substitutions in the investigated sequences would cause a change in potential O-glycosylation and N-glycosylation profiles from prototype ON1. The predominance of the ON1 and BA9 genotype of RSV-A in Jeddah compared to previous Saudi studies showing predominance of the NA1 genotype for group A. This difference in genotype prevalence could be due to fast spread of the ON1 genotype worldwide or due to the flux of travelers through Jeddah during hajj/umrah compared to Riyadh and Taif. This shift in genotype distribution requires continuous surveillance for genetic characterization of circulating respiratory infections including RSV. These findings may contribute to the understanding of RSV evolution and to the potential development of a vaccine against RSV.
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Tsergouli K, Pappa S, Haidopoulou K, Gogou M, Giannopoulos A, Papa A. Respiratory Syncytial Virus in Greece, 2016-2018. Intervirology 2020; 62:210-215. [PMID: 32348998 DOI: 10.1159/000506049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/18/2020] [Indexed: 01/03/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of acute bronchiolitis in infants and young children. Children under the age of 2 years, hospitalized for bronchiolitis in the pediatric clinic of a tertiary hospital in northern Greece, were tested for RSV infection during two RSV seasons (2016-2017 and 2017-2018). RSV was detected in 37 of 71 (52.1%) patients, most of them younger than 6 months. Both RSV subtypes were detected - RSV-A (54.1%) and RSV-B (45.9%) - with predominance of RSV-A during the 2016-2017 and RSV-B during the 2017-2018 season. RSV-A and RSV-B sequences clustered within the ON1 and BA genotypes, respectively. Compared to the prototype strains, several amino acid substitutions were observed in the duplication region of the G gene. The study provides a first insight into the molecular epidemiology of RSV in Greece.
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Affiliation(s)
- Katerina Tsergouli
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Pappa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Katerina Haidopoulou
- Second Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Gogou
- Second Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Giannopoulos
- Second Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece,
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Zhao T, Ye Z, Wang B, Cui Y, Nie Y, Yang B, Chen K, Zhang H, Hu F, Yu F. Virus isolation and genotype identification of human respiratory syncytial virus in Guizhou Province, China. Braz J Infect Dis 2019; 23:427-434. [PMID: 31734172 PMCID: PMC9428243 DOI: 10.1016/j.bjid.2019.10.007] [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: 06/24/2019] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 11/30/2022] Open
Abstract
To investigate the genetic variation and molecular epidemiology characteristics of Human Respiratory Syncytial Virus (HRSV) in Guizhou Province, nasopharyngeal aspirates were collected from patients with acute respiratory infection (ARI) in Guizhou Provincial People's Hospital, from December 2017 to March 2018, and inoculated to Hep-2 cells to isolate HRSV. Cells that showed cytopathic effect (CPE) were then confirmed by indirect immunofluorescence assay and reverse transcription. The sequence of the PCR products was determined for HRSV isolates, and the genetic variation was analyzed. Out of 196 nasopharyngeal aspirate samples, HRSV were isolated in 39. The second hypervariable region at the 3′ terminal of glycoprotein gene (HVR2) sequence analysis showed that subgroup A was dominant. Seventy-nine percent of the isolates belonged to subgroup A, ON1 genotype, and 21 % belonged to subgroup B, BA9 genotype, which indicates that the dominant HRSV circulating in Guizhou Province was subgroup A, genotype ON1, co-circulating with a less prevalent subgroup B, genotype BA9.
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Affiliation(s)
- Ting Zhao
- Guizhou University, Medical College, Guiyang, China; Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina.
| | - Zhixu Ye
- Guizhou University, Guizhou Provincial People's Hospital, Department of Pediatrics, Guiyang, China; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Binlin Wang
- People's Hospital of QianNan, Department of Clinical Labotatory, Guizhou Province, China
| | - Yuxia Cui
- Guizhou University, Guizhou Provincial People's Hospital, Department of Pediatrics, Guiyang, China
| | - Yingjie Nie
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Bin Yang
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Kun Chen
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Hua Zhang
- Guizhou University, Guizhou Provincial People's Hospital, Department of Clinical Laboratory, Guiyang, China
| | - Fangfang Hu
- Guizhou University, Guizhou Provincial People's Hospital, Department of Clinical Laboratory, Guiyang, China
| | - Fuxun Yu
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
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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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Sáez-López E, Cristóvão P, Costa I, Pechirra P, Conde P, Guiomar R, Peres MJ, Viseu R, Lopes P, Soares V, Vale F, Fonseca P, Freitas L, Alves J, Pessanha MA, Toscano C, Mota-Vieira L, Veloso RC, Côrte-Real R, Branquinho P, Pereira-Vaz J, Rodrigues F, Cunha M, Martins L, Mota P, Couto AR, Bruges-Armas J, Almeida S, Rodrigues D. Epidemiology and genetic variability of respiratory syncytial virus in Portugal, 2014-2018. J Clin Virol 2019; 121:104200. [PMID: 31707201 PMCID: PMC7106440 DOI: 10.1016/j.jcv.2019.104200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is associated with substantial morbidity and mortality since it is a predominant viral agent causing respiratory tract infections in infants, young children and the elderly. Considering the availability of the RSV vaccines in the coming years, molecular understanding in RSV is necessary. OBJECTIVE The objective of the present study was to describe RSV epidemiology and genotype variability in Portugal during the 2014/15-2017/18 period. MATERIAL AND METHODS Epidemiological data and RSV-positive samples from patients with a respiratory infection were collected through the non-sentinel and sentinel influenza surveillance system (ISS). RSV detection, subtyping in A and B, and sequencing of the second hypervariable region (HVR2) of G gene were performed by molecular methods. Phylogenetic trees were generated using the Neighbor-Joining method and p-distance model on MEGA 7.0. RESULTS RSV prevalence varied between the sentinel (2.5%, 97/3891) and the non-sentinel ISS (20.7%, 3138/16779), being higher (P < 0.0001) among children aged <5 years. Bronchiolitis (62.9%, 183/291) and influenza-like illness (24.6%, 14/57) were associated (P < 0.0001) with RSV laboratory confirmation among children aged <6 months and adults ≥65 years, respectively. The HVR2 was sequenced for 562 samples. RSV-A (46.4%, 261/562) and RSV-B (53.6%, 301/562) strains clustered mainly to ON1 (89.2%, 233/261) and BA9 (92%, 277/301) genotypes, respectively, although NA1 and BA10 were also present until 2015/2016. CONCLUSION The sequence and phylogenetic analysis reflected the relatively high diversity of Portuguese RSV strains. BA9 and ON1 genotypes, which have been circulating in Portugal since 2010/2011 and 2011/2012 respectively, predominated during the whole study period.
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Affiliation(s)
- Emma Sáez-López
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal; European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 16973, Solna, Sweden.
| | - Paula Cristóvão
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Inês Costa
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Pedro Pechirra
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Patrícia Conde
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Raquel Guiomar
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
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Streng A, Goettler D, Haerlein M, Lehmann L, Ulrich K, Prifert C, Krempl C, Weißbrich B, Liese JG. Spread and clinical severity of respiratory syncytial virus A genotype ON1 in Germany, 2011-2017. BMC Infect Dis 2019; 19:613. [PMID: 31299924 PMCID: PMC6624929 DOI: 10.1186/s12879-019-4266-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Background The Respiratory Syncytial Virus (RSV) A genotype ON1, which was first detected in Ontario (Canada) in 2010/11, appeared in Germany in 2011/12. Preliminary observations suggested a higher clinical severity in children infected with this new genotype. We investigated spread and disease severity of RSV-A ON1 in pediatric in- and outpatient settings. Methods During 2010/11 to 2016/17, clinical characteristics and respiratory samples from children with acute respiratory tract infections (RTI) were obtained from ongoing surveillance studies in 33 pediatric practices (PP), one pediatric hospital ward (PW) and 23 pediatric intensive care units (PICU) in Germany. RSV was detected in the respiratory samples by PCR; genotypes were identified by sequencing. Within each setting, clinical severity markers were compared between RSV-A ON1 and RSV-A non-ON1 genotypes. Results A total of 603 children with RSV-RTI were included (132 children in PP, 288 in PW, and 183 in PICU). Of these children, 341 (56.6%) were infected with RSV-A, 235 (39.0%) with RSV-B, and one child (0.2%) with both RSV-A and RSV-B; in 26 (4.3%) children, the subtype could not be identified. In the 341 RSV-A positive samples, genotype ON1 was detected in 247 (72.4%), NA1 in 92 (26.9%), and GA5 in 2 children (0.6%). RSV-A ON1, rarely observed in 2011/12, was the predominant RSV-A genotype in all settings by 2012/13 and remained predominant until 2016/17. Children in PP or PW infected with RSV-A ON1 did not show a more severe clinical course of disease compared with RSV-A non-ON1 infections. In the PICU group, hospital stay was one day longer (median 8 days, inter-quartile range (IQR) 7–12 vs. 7 days, IQR 5–9; p = 0.02) and duration of oxygen treatment two days longer (median 6 days, IQR 4–9 vs. 4 days, IQR 2–6; p = 0.03) for children infected with RSV-A ON1. Conclusions In children, RSV-A ON1 largely replaced RSV-A non-ON1 genotypes within two seasons and remained the predominant RSV-A genotype in Germany during subsequent seasons. A higher clinical severity of RSV-A ON1 was observed within the group of children receiving PICU treatment, whereas in other settings clinical severity of RSV-A ON1 and non-ON1 genotypes was largely similar. Electronic supplementary material The online version of this article (10.1186/s12879-019-4266-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Streng
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany.
| | - David Goettler
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Miriam Haerlein
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Lisa Lehmann
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Kristina Ulrich
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Christiane Prifert
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Christine Krempl
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Benedikt Weißbrich
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Johannes G Liese
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
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Bin Lu, Liu H, Tabor DE, Tovchigrechko A, Qi Y, Ruzin A, Esser MT, Jin H. Emergence of new antigenic epitopes in the glycoproteins of human respiratory syncytial virus collected from a US surveillance study, 2015-17. Sci Rep 2019; 9:3898. [PMID: 30846850 PMCID: PMC6405860 DOI: 10.1038/s41598-019-40387-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/11/2019] [Indexed: 12/31/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a significant cause of lower respiratory tract infection in infants and elderly. To understand the evolution of neutralizing epitopes on the RSV glycoprotein (G) and fusion (F) proteins, we conducted a multi-year surveillance program (OUTSMART-RSV) in the US. Analysis of 1,146 RSV samples from 2015-2017 revealed a slight shift in prevalence from RSV A (58.7%) to B (53.7%) between the two seasons. RSV B was more prevalent in elderly (52.9% and 73.4%). Approximately 1% of the samples contained both RSV A and B viruses. All RSV A isolates were ON1 and almost all the B isolates were BA9 genotypes. Compared with the 2013 reference sequences, changes at the F antigenic sites of RSV B were greater than RSV A, which mainly occurred at antigenic sites V (L172Q/S173L at 99.6%), Ø (I206M/Q209K at 18.6%) and IV (E463D at 7%) of RSV B F. Sequence diversities in the G protein second hypervariable region were observed in the duplicated regions for RSV A and B, and at the G stop codon resulting in extension of 7 amino acids (22.1%) for RSV B in 2016-17. Thus, RSV surface glycoproteins are continuously evolving, and continued surveillance is important for the clinical evaluation of immunoprophylactic products.
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Affiliation(s)
- Bin Lu
- MedImmune/AstraZeneca, South San Francisco, CA, USA
| | - Hui Liu
- MedImmune/AstraZeneca, South San Francisco, CA, USA
| | | | | | - Yanping Qi
- MedImmune/AstraZeneca, South San Francisco, CA, USA
| | | | | | - Hong Jin
- MedImmune/AstraZeneca, South San Francisco, CA, USA.
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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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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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Altered regulatory cytokine profiles in cases of pediatric respiratory syncytial virus infection. Cytokine 2018; 103:57-62. [PMID: 29324262 PMCID: PMC7130056 DOI: 10.1016/j.cyto.2017.12.028] [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: 08/30/2017] [Revised: 12/25/2017] [Accepted: 12/27/2017] [Indexed: 12/11/2022]
Abstract
Objectives Regulatory cytokines are associated with viral infection. The objective of this study was to evaluate the relation between serum regulatory cytokines concentrations and respiratory syncytial virus (RSV) disease. Methods We enrolled 325 children aged < 24 months who were diagnosed with acute respiratory tract infection. Twenty age-matched healthy children were enrolled as controls. Nasopharyngeal swabs were analyzed to identify virus by reverse transcription polymerase chain reaction, and blood samples were taken to quantify the regulatory cytokine concentrations, including interleukin (IL)-35, IL-10 and transforming growth factor (TGF)-β1 using the Bio-Plex immunoassay or enzyme-linked immunosorbent assay. Results RSV disease was associated with a great regulatory cytokine response than healthy children, among 89 RSV-infected patients, serum IL-35 (P = .0001) and IL-10 (P = .006) was significantly elevated in comparison with healthy controls. Young children (0< age ≤6 months) with RSV infection had significantly lower IL-35 and IL-10 expression but needed more oxygen therapy and more severe disease comparing with older children (12< age <24 months). Comparing with mild group, the expression levels of IL-10 were significantly lower in children with moderate and severe disease (P = .012 and P = .005, respectively). And levels of IL-10 was inversely associated with total duration of RSV infection symptoms (r = − 0.311, P = .019). Conclusion Children with RSV infected had increased serum regulatory cytokine IL-10 and IL-35 concentrations. Elevated expression of IL-10 and IL-35 were contributed to protect hypoxia and reduce the severity of disease.
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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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Zou L, Yi L, Wu J, Song Y, Huang G, Zhang X, Liang L, Ni H, Pybus OG, Ke C, Lu J. Evolution and Transmission of Respiratory Syncytial Group A (RSV-A) Viruses in Guangdong, China 2008-2015. Front Microbiol 2016; 7:1263. [PMID: 27574518 PMCID: PMC4983572 DOI: 10.3389/fmicb.2016.01263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/02/2016] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial viruses (RSVs) including subgroups A (RSV-A) and B (RSV-B) are an important cause of acute respiratory tract infections worldwide. RSV-A include major epidemic strains. Fundamental questions concerning the evolution, persistence and transmission of RSV-A are critical for disease control and prevention, yet remain unanswered. In this study, we generated 64 complete G gene sequences of RSV-A strains collected between 2008 and 2015 in Guangdong, China. Phylogenetic analysis was undertaken by incorporating 572 publicly available RSV-A sequences. Current data indicate that genotypes GA1, GA4, and GA5 are endemic with limited epidemic activity. In contrast, the GA2 genotype which likely originated in 1980 has spread rapidly and caused epidemics worldwide. By analyzing GA2 genotype sequences across epidemic seasons within Guangdong, we find that RSV-A epidemics in Guangdong are caused by a combination of virus importation and local persistence, although the magnitude of the latter is likely overestimated due to infrequent sampling in other regions. Our results provide new insights into RSV-A evolution and transmission at global and local scales and highlights the rapid and wide spread of genotype GA2 compared to other genotypes. In order to control RSV transmission and outbreak, both local persistence and external introduction should be taken into account when designing optimal strategies.
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Affiliation(s)
- Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Yingchao Song
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Guofeng Huang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Xin Zhang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Lijun Liang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Hanzhong Ni
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | | | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Department of Zoology, University of OxfordOxford, UK
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