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Amjad MN, Wang J, Ashraf MA, Shen B, Din GU, Raza MA, Shoaib M, Yue L, Chen L, Xu H, Dong W, Hu Y. Evolutionary trends of respiratory syncytial viruses: Insights from large-scale surveillance and molecular dynamics of G glycoprotein. Heliyon 2024; 10:e30886. [PMID: 38784562 PMCID: PMC11112325 DOI: 10.1016/j.heliyon.2024.e30886] [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: 02/26/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Human respiratory syncytial virus (RSV) is an underlying cause of lower respiratory illnesses in children, elderly and immunocompromised adults. RSV contains multiple structural and non-structural proteins with two major glycoproteins that control the initial phase of infection, fusion glycoprotein and the attachment (G) glycoprotein. G protein attaches to the ciliated cells of airways initiating the infection. The hypervariable G protein plays a vital role in evolution of RSV strains. We employed multiple bioinformatics tools on systematically accessed large-scale data to evaluate mutations, evolutionary history, and phylodynamics of RSV. Mutational analysis of central conserved region (CCR) on G protein-coding sequences between 163 and 189 positions revealed frequent mutations at site 178 in human RSV (hRSV) A while arginine to glutamine substitutions at site 180 positions in hRSV B, remained prevalent from 2009 to 2014. Phylogenetic analysis indicates multiple signature mutations within G protein responsible for diversification of clades. The USA and China have highest number of surveillance records, followed by Kenya. Markov Chain Monte Carlo Bayesian skyline plot revealed that RSV A evolved steadily from 1990 to 2000, and rapidly between 2003 and 2005. Evolution of RSV B continued from 2003 to 2022, with a high evolution stage from 2016 to 2020. Throughout evolution, cysteine residues maintained their strict conserved states while CCR has an entropy value of 0.0039(±0.0005). This study concludes the notion that RSV G glycoprotein is continuously evolving while the CCR region of G protein maintains its conserved state providing an opportunity for CCR-specific monoclonal antibodys (mAbs) and inhibitors as potential candidates for immunoprophylaxis.
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Affiliation(s)
- Muhammad Nabeel Amjad
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Awais Ashraf
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bei Shen
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
| | - Ghayyas ud Din
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Asif Raza
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Shoaib
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Lihuan Yue
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
| | - Lingdie Chen
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huiting Xu
- Pediatric Department, Nanxiang Branch of Ruijin Hospital, Shanghai, 201802, China
| | - Wei Dong
- Pediatric Department, Nanxiang Branch of Ruijin Hospital, Shanghai, 201802, China
| | - Yihong Hu
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, China
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Guo CY, Zhang Y, Zhang YY, Zhao W, Peng XL, Zheng YP, Fu YH, Yu JM, He JS. Comparative analysis of human respiratory syncytial virus evolutionary patterns during the COVID-19 pandemic and pre-pandemic periods. Front Microbiol 2023; 14:1298026. [PMID: 38111642 PMCID: PMC10725919 DOI: 10.3389/fmicb.2023.1298026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023] Open
Abstract
The COVID-19 pandemic has resulted in the implementation of strict mitigation measures that have impacted the transmission dynamics of human respiratory syncytial virus (HRSV). The measures also have the potential to influence the evolutionary patterns of the virus. In this study, we conducted a comprehensive analysis comparing genomic variations and evolving characteristics of its neutralizing antigens, specifically F and G proteins, before and during the COVID-19 pandemic. Our findings showed that both HRSV A and B exhibited an overall chronological evolutionary pattern. For the sequences obtained during the pandemic period (2019-2022), we observed that the HRSV A distributed in A23 genotype, but formed into three subclusters; whereas the HRSV B sequences were relatively concentrated within genotype B6. Additionally, multiple positively selected sites were detected on F and G proteins but none were located at neutralizing antigenic sites of the F protein. Notably, amino acids within antigenic site III, IV, and V of F protein remained strictly conserved, while some substitutions occurred over time on antigenic site Ø, I, II and VIII; substitution S389P on antigenic site I of HRSV B occurred during the pandemic period with nearly 50% frequency. However, further analysis revealed no substitutions have altered the structural conformations of the antigenic sites, the vial antigenicity has not been changed. We inferred that the intensive public health interventions during the COVID-19 pandemic did not affect the evolutionary mode of HRSV.
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Affiliation(s)
| | | | | | | | | | | | | | - Jie-mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jin-sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
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Lin WH, Wu FT, Chen YY, Wang CW, Lin HC, Kuo CC, Lai WC, Lin FJ, Tiew WT, Tsai AL, Ho KT, Kuo TY, Li CH, Wu CY, Pan YJ, Tsao KC, Hsieh YC. Unprecedented outbreak of respiratory syncytial virus in Taiwan associated with ON1 variant emergence between 2010 and 2020. Emerg Microbes Infect 2022; 11:1000-1009. [PMID: 35293267 PMCID: PMC8979508 DOI: 10.1080/22221751.2022.2054365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An outbreak of respiratory syncytial virus (RSV) has been observed in Taiwan since August 2020. We reviewed a central laboratory-based surveillance network established over 20 years by Taiwan Centres for Disease Control for respiratory viral pathogens between 2010 and 2020.A retrospective study of children <5 years old hospitalized with RSV infection at Chang Gung Memorial Hospital between 2018 and 2020 was conducted, and samples positive for RSV-A were sequenced. Clinical data were obtained and stratified by genotype and year.Data from 2020 showed an approximately 4-fold surge in RSV cases compared to 2010 in Taiwan, surpassing previous years during which ON1 was prevalent. Phylogenetic analysis of G protein showed that novel ON1 variants were clustered separately from those of 2018 and 2019 seasons and ON1 reference strains. The variant G protein carried six amino acid changes that emerged gradually in 2019; high consistency was observed in 2020. A unique substitution, E257K, was observed in 2020 exclusively. The F protein of the variant carried T12I and H514N substitutions, which weren't at antigenic sites. In terms of multivariate analysis, age (OR: 0.97; 95% CI: 0.94-0.99; p = 0.02) and 2020 ON1 variant (OR:2.52; 95% CI:1.13-5.63; p = 0.025) were independently associated with oxygen saturation <94% during hospitalization.The 2020 ON1 variant didn't show higher replication or virulence compared with those in 2018 in our study. The unprecedented 2020 RSV epidemic may attribute to antigenic changes and lack of interferon-stimulated immunity induced by seasonal circulating virus under non-pharmaceutical intervention.
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Affiliation(s)
- Wei-Hsuan Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Fang-Tzy Wu
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Wei Wang
- Departments of Anatomic Pathology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ho-Chen Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Chia Kuo
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Chun Lai
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Fang-Ju Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Wan-Tin Tiew
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - An-Li Tsai
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Ta Ho
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ting-Yu Kuo
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chung-Hao Li
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ching-Yi Wu
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yi-Jiun Pan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Kuo-Chien Tsao
- Research Centre for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan.,Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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4
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Lin TY, Chi H, Kuo CY, Tsai HP, Wang JR, Liu CC, Shen CF. Outbreak of respiratory syncytial virus subtype ON1 among children during COVID-19 pandemic in Southern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1168-1179. [PMID: 36137926 DOI: 10.1016/j.jmii.2022.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND The regional respiratory syncytial virus (RSV) outbreak in southern Taiwan in late 2020 followed the surge of RSV cases in the national surveillance data and displayed distinct clinical features. This study investigated RSV epidemiology in the most recent five years and compared the clinical manifestations of this outbreak with non-outbreak period. METHODS Medical records of RSV-infected children at the National Cheng Kung University Hospital from January 2016 to December 2020 were retrospectively retrieved from hospital-based electronic medical database. Cases of RSV infection were identified by RSV antigen positive and/or RSV isolated from respiratory specimens. The demographic, clinical presentations, and laboratory data were recorded. The RSV isolates in 2020 was sequenced for phylogenetic analysis. RESULTS Overall, 442 RSV-infected cases were retrieved and 42.1% (186 cases) clustered in late 2020. The 2020 outbreak started in September, peaked in November, and lasted for 3 months. 2020 RSV-infected children were older (2.3 ± 2.2 years vs. 1.0 ± 1.0 years), more likely to be diagnosed with bronchopneumonia (57.5% vs. 31.6%), but also had a lower hospitalization rate, shorter hospital stay, less oxygen use, and less respiratory distress than those in 2016-2019 (all p value < 0.05). The RSV isolates in 2020 belonged to RSV-A subtype ON1 but were phylogenetically distinct from the ON1 strains prevalent in Taiwan previously. CONCLUSION The 2020 RSV outbreak was led by the novel RSV-A subtype ON1 variant with clinical manifestations distinct from previous years. Continuous surveillance of new emerging variants of respiratory viruses in the post-pandemic era is warranted.
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Affiliation(s)
- Ting-Yu Lin
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin Chi
- Department of Medicine, MacKay Medicine College, New Taipei, Taiwan; Department of Pediatrics, MacKay Children's Hospital and MacKay Memorial Hospital, Taipei, Taiwan
| | - Cheng-Yen Kuo
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.
| | - Ching-Fen Shen
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Cantú-Flores K, Rivera-Alfaro G, Muñoz-Escalante JC, Noyola DE. Global distribution of respiratory syncytial virus A and B infections: a systematic review. Pathog Glob Health 2022; 116:398-409. [PMID: 35156555 PMCID: PMC9518599 DOI: 10.1080/20477724.2022.2038053] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the main cause of severe respiratory infections in young children. The need for global epidemiologic data regarding RSV has been increasingly recognized. RSV A infections are reported more frequently than RSV B. Nonetheless, the temporal distribution of infections caused by both RSV groups has not been investigated globally. A systematic review was carried out regarding published studies on RSV A and B epidemiology, as well as RSV G gene ectodomain sequence data available at GenBank. A total of 76,668 [45,990 (60%) RSV A and 30,678 (40%) RSV B] positive samples from 83 countries were identified and included in the analysis. Genotype assignment was obtained in 5,340 RSV A and 2,518 RSV B sequences. Two patterns of RSV circulation were observed: continuous seasons with RSV A predominance and alternate predominance of RSV A and B. These patterns were observed in all regions, but the predominant RSV group seldom coincided in all continents during a given year or season. The most frequently identified RSV A genotype was NA1 (including ON1 viruses) (76.30%), and the most frequently identified RSV B genotype was BA (70.65%). Multiple genotypes circulated simultaneously throughout the evolutionary history of RSV, but genotype diversity decreased after the year 2000. The classification of RSV group and genotype is important for the development of vaccines, as well as to understand viral dynamics. This study displays the global and continental RSV circulation patterns from the first report of human RSV infection until the end of 2020.
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Affiliation(s)
- Karla Cantú-Flores
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Gerardo Rivera-Alfaro
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Juan Carlos Muñoz-Escalante
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Daniel E. Noyola
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico,CONTACT Daniel E. Noyola Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, Avenida Venustiano Carranza 2405, San Luis Potosí78210, México
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6
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Wetzke M, Funken D, Lange M, Bejo L, Haid S, Monteiro JGT, Schütz K, Happle C, Schulz TF, Seidenberg J, Pietschmann T, Hansen G. IRIS: Infection with RespIratory Syncytial Virus in infants-a prospective observational cohort study. BMC Pulm Med 2022; 22:88. [PMID: 35291998 PMCID: PMC8922907 DOI: 10.1186/s12890-022-01842-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infection in infants. Globally, RSV is responsible for approximately 3.2 million hospital admissions and about 60,000 in-hospital deaths per year. METHODS Infection with RespIratory Syncytial Virus (IRIS) is an observational, multi-centre study enrolling infants with severe RSV infection and healthy controls. Inclusion criteria are age between 0 and 36 months and hospitalisation due to RSV infection at three German sites. Exclusion criteria are premature birth, congenital or acquired bronchopulmonary or cardiac diseases, and immunodeficiency. Healthy control probands are enrolled via recruitment of patients undergoing routine surgical procedures. Blood and respiratory specimens are collected upon admission, and RSV and other pathogens are analysed by multiplex polymerase chain reaction. Different biomaterials, including plasma, nasal lining fluid, blood cells, DNA, and RNA specimens, are sampled in a dedicated biobank. Detailed information on demographic characteristics and medical history is recorded, and comprehensive clinical data, including vital signs, medication, and interventions. DISCUSSION The IRIS study aims to discover host and viral factors controlling RSV disease courses in infants. The approach including multi-omics characterisation in clinically well-characterized children with RSV bronchiolitis seeks to improve our understanding of the immune response against this virus. It may disclose novel diagnostic and treatment approaches for respiratory infections in infants. TRIAL REGISTRATION ClinicalTrials.gov, NCT04925310. Registered 01 October 2021-Retrospectively registered. https://clinicaltrials.gov/ct2/show/NCT04925310?cond=NCT04925310&draw=2&rank=1.
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Affiliation(s)
- Martin Wetzke
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany.,German Center for Infection Research (DZIF), Site Hanover-Brunswick, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Dominik Funken
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
| | - Mathias Lange
- Department of Pediatric Pneumology and Allergology, Universitätsklinik für Kinder- und Jugendmedizin Oldenburg, Oldenburg, Germany
| | - Levente Bejo
- Helios Childrens Hospital Hildesheim, Hildesheim, Germany
| | - Sibylle Haid
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Joao G Tereno Monteiro
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Katharina Schütz
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
| | - Christine Happle
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Thomas F Schulz
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.,Institute of Virology, Hannover Medical School, 30625, Hannover, Germany
| | - Jürgen Seidenberg
- Department of Pediatric Pneumology and Allergology, Universitätsklinik für Kinder- und Jugendmedizin Oldenburg, Oldenburg, Germany
| | - Thomas Pietschmann
- German Center for Infection Research (DZIF), Site Hanover-Brunswick, Germany.,Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany. .,Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany. .,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.
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7
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Wangui J, Nokes DJ, Mobegi VA, Otieno JR, Agoti CN, Ngeranwa JJN, Bulimo WD. Spatial-temporal distribution and sequence diversity of group a human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype. Influenza Other Respir Viruses 2021; 16:501-510. [PMID: 34962085 PMCID: PMC8983921 DOI: 10.1111/irv.12948] [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: 11/15/2021] [Accepted: 12/05/2021] [Indexed: 12/02/2022] Open
Abstract
Background Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial–temporal distribution as defined by its genetic diversity. Methods A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT‐PCR (reverse transcriptase polymerase chain reaction). A segment of the G‐gene was amplified using one‐step RT‐PCR and sequenced by Sanger di‐deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction. Results Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%), and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi[π]) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes. Conclusions HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2, and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing toward the Western zones and decreasing toward the Eastern zones of the country.
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Affiliation(s)
- Julia Wangui
- Department of Biochemistry, Kenyatta University, Nairobi, Kenya.,Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - D James Nokes
- Department of Epidemiology and Demography, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Victor A Mobegi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - James R Otieno
- Department of Epidemiology and Demography, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.,Department of Epidemiology and Demography, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Wallace D Bulimo
- Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
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8
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Lee CY, Fang YP, Wang LC, Chou TY, Liu HF. Genetic Diversity and Molecular Epidemiology of Circulating Respiratory Syncytial Virus in Central Taiwan, 2008-2017. Viruses 2021; 14:v14010032. [PMID: 35062237 PMCID: PMC8777914 DOI: 10.3390/v14010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/22/2022] Open
Abstract
In this study, we investigated the molecular evolution and phylodynamics of respiratory syncytial virus (RSV) over 10 consecutive seasons (2008–2017) and the genetic variability of the RSV genotypes ON1 and BA in central Taiwan. The ectodomain region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the second hypervariable region of the G protein in RSV ON1 and BA were analyzed. A total of 132 RSV-A and 81 RSV-B isolates were obtained. Phylogenetic analysis revealed that the NA1, ON1, and BA9 genotypes were responsible for the RSV epidemics in central Taiwan in the study period. For RSV-A, the NA1 genotype predominated during the 2008–2011 seasons. The ON1 genotype was first detected in 2011 and replaced NA1 after 2012. For RSV-B, the BA9 and BA10 genotypes cocirculated from 2008 to 2010, but the BA9 genotype has predominated since 2012. Amino acid sequence alignments revealed the continuous evolution of the G gene in the ectodomain region. The predicted N-glycosylation sites were relatively conserved in the ON1 (site 237 and 318) and BA9 (site 296 and 310) genotype strains. Our results contribute to the understanding and prediction of the temporal evolution of RSV at the local level.
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Affiliation(s)
- Chun-Yi Lee
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua 505029, Taiwan; (C.-Y.L.); (Y.-P.F.)
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
| | - Yu-Ping Fang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua 505029, Taiwan; (C.-Y.L.); (Y.-P.F.)
| | - Li-Chung Wang
- Department of Pathology and Laboratory Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
| | - Teh-Ying Chou
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, Mackay Memorial Hospital, Taipei 25160, Taiwan
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City 25245, Taiwan
- Correspondence:
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Lee CY, Wu TH, Fang YP, Chang JC, Wang HC, Lin SJ, Mai CH, Chang YC, Chou TY. Delayed respiratory syncytial virus outbreak in 2020 in Taiwan was correlated with two novel RSV-A genotype ON1 variants. Influenza Other Respir Viruses 2021; 16:511-520. [PMID: 34913593 PMCID: PMC8983888 DOI: 10.1111/irv.12951] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/05/2021] [Indexed: 11/29/2022] Open
Abstract
Background Human respiratory syncytial virus (RSV) is a leading pathogen of acute respiratory tract disease among infants and young children. Compared with previous seasons, RSV outbreaks in Taiwan during the 2020–2021 season were delayed because of COVID‐19 mitigation measures. We conducted this study to determine the association of viral factors with clinical characteristics of preschool children with RSV infection. Methods We performed a molecular epidemiology analysis of RSV among inpatient preschool children in Taiwan. In 80 nasopharyngeal samples positive for RSV, we sequenced and analyzed viral genotypes according to patient data. Patients' clinical data were obtained from medical files, and their clinical profiles were compared with those of RSV cases recorded during the 2014–2017 seasons. Results Phylogenetic analysis revealed that among the RSV‐positive samples, all RSV strains identified during the 2020–2021 season belonged to the ON1 genotype. Most of the Taiwan ON1 strains were categorized into two well‐supported clusters with distinct G protein amino acid substitution patterns that had never been demonstrated previously. Furthermore, the proportion of cases among children aged >24 months increased (P < 0.001). Compared with patients infected during the 2014–2017 seasons, patients infected during the 2020–2021 season were hospitalized for shorter days from hospital admission to dereference (P = 0.004) and had a greater need for oxygen supplements (P = 0.021) and systemic steroid therapy (P = 0.026). Conclusion The delayed 2020–2021 RSV outbreak in Taiwan was caused by two novel RSV ON1.1 variants. How the change in RSV epidemiology affects future RSV outbreaks warrants exploration.
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Affiliation(s)
- Chun Yi Lee
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tsung Hua Wu
- Department of Pediatrics, Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Yu Ping Fang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Jih Chin Chang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Hung Chun Wang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Shou Ju Lin
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Chen Hao Mai
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Yu Chuan Chang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Teh Ying Chou
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
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Evolutionary dynamics of group A and B respiratory syncytial virus in China, 2009-2018. Arch Virol 2021; 166:2407-2418. [PMID: 34131849 DOI: 10.1007/s00705-021-05139-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Respiratory syncytial virus (RSV) is a major cause of acute respiratory tract infections in children and is a public health threat globally. To investigate the spatiotemporal dynamics of RSV evolution, we performed systematic phylogenetic analysis using all available sequences from the GenBank database, together with sequences from Shanghai, China. Both RSV-A and RSV-B appear to have originated in North America, with an inferred origin time of 1954.0 (1938.7-1967.6) and 1969.7 (1962.6-1975.5), respectively. BA-like strains of RSV-B, with a 60-nt insertion, and the ON1 strain of RSV-A, with a 72-nt insertion, emerged in 1997.6 (1996.2-1998.6) and 2010.1 (2009.1-2010.3), respectively. Since their origin, both genotypes have gradually replaced the former circulating genotypes to become the dominant strain. The population dynamic of RSV-A showed a seasonal epidemic pattern with obvious expansion in the periods of 2006-2007, 2010-2011, 2011-2012, and 2013-2014. Thirty fixed amino acid substitutions were identified during the divergence of NA4 from GA1 genotypes of RSV-A, and 13 were found during the divergence of SAB4 from GB1 of RSV-B. Importantly, ongoing evolution has occurred since the emergence of ON1, including four amino acid substitutions (I208L, E232G, T253K, and P314L). RSV-A genotypes GA5, NA4, NA1, and ON1 and RSV-B genotypes CB1, SAB4, BA-C, BA10, BA7, and BA9 were co-circulating in China from 2005 to 2015. In particular, RSV-A genotype ON1 was first detected in China in 2011, and it completely replaced GA2 to become the predominant strain after 2016. These data provide important insights into the evolution and epidemiology of RSV.
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Evolutionary analysis of human respiratory syncytial virus collected in Myanmar between 2015 and 2018. INFECTION GENETICS AND EVOLUTION 2021; 93:104927. [PMID: 34020068 DOI: 10.1016/j.meegid.2021.104927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/24/2022]
Abstract
We studied genetic variation in the second hypervariable region (HVR) of the G gene of human respiratory syncytial virus (HRSV) from 1701 nasal swab samples collected from outpatients with acute respiratory infections at two general hospitals in the cities Yangon and Pyinmana in Myanmar from 2015 to 2018. HRSV genotypes were characterized using phylogenetic trees constructed using the maximum likelihood method. Time-scale phylogenetic tree analyses were performed using the Bayesian Markov chain Monte Carlo method. In total, 244 (14.3%) samples were HRSV-positive and were classified as HRSV-A (n = 84, 34.4%), HRSV-B (n = 158, 64.8%), and co-detection of HRSV-A/HRSV-B (n = 2, 0.8%). HRSV epidemics occurred seasonally between July (1.9%, 15/785) and August (10.5%, 108/1028), with peak infections in September (35.8%, 149/416) and October (58.2%, 89/153). HRSV infection rate was higher in children ≥1 year of age than in those <1 year of age (70.5% vs. 29.5%). The most common HRSV symptoms in children were cough (80%-90%) and rhinorrhea (70%-100%). The predominant genotypes were ON1for HRSV-A (78%) and BA9 for HRSV-B (64%). Time to the most recent common ancestor was 2014 (95% highest posterior density [HPD], 2012-2015) for HRSV-A ON1 and 2009 (95% HPD, 2004-2012) for HRSV-B BA9. The mean evolutionary rate (substitutions/site/year) for HRSV-B (2.12 × 10-2, 95% HPD, 8.53 × 10-3-3.63 × 10-2) was slightly higher than that for HRSV-A (1.39 × 10-2, 95% HPD, 6.03 × 10-3-2.12 × 10-2). The estimated effective population size (diversity) for HRSV-A increased from 2015 to 2016 and declined in mid-2018, whereas HRSV-B diversity was constant in 2015 and 2016 and increased in mid-2017. In conclusion, the dominant HRSV-A and HRSV-B genotypes in Myanmar were ON1 and BA9, respectively, between 2015 and 2018. HRSV-B evolved slightly faster than HRSV-A and exhibited unique phylogenetic characteristics.
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