1
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Musa AO, Faber SR, Forrest K, Smith KP, Sengupta S, López CB. Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590570. [PMID: 38712045 PMCID: PMC11071361 DOI: 10.1101/2024.04.22.590570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Respiratory syncytial virus is a common cause of respiratory infection that often leads to hospitalization of infected younger children and older adults. RSV is classified into two strains, A and B, each with several subgroups or genotypes. One issue with the definition of these subgroups is the lack of a unified method of identification or genotyping. We propose that genotyping strategies based on the genes coding for replication-associated proteins could provide critical information on the replication capacity of the distinct subgroup, while clearly distinguishing genotypes. Here, we analyzed the virus replication-associated genes N, P, M2, and L from de novo assembled RSV A sequences obtained from 31 newly sequenced samples from hospitalized patients in Philadelphia and 78 additional publicly available sequences from different geographic locations within the US. In-depth analysis and annotation of the protein variants in L and the other replication-associated proteins N, P, M2-1, and M2-2 identified the polymerase protein L as a robust target for genotyping RSV subgroups. Importantly, our analysis revealed non-synonymous variations in L that were consistently accompanied by conserved changes in its co-factor P or the M2-2 protein, suggesting associations and interactions between specific domains of these proteins. These results highlight L as an alternative to other RSV genotyping targets and demonstrate the value of in-depth analyses and annotations of RSV sequences as it can serve as a foundation for subsequent in vitro and clinical studies on the efficiency of the polymerase and fitness of different virus isolates.
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Affiliation(s)
- Abdulafiz O. Musa
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Sydney R. Faber
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Kaitlyn Forrest
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kenneth P. Smith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Infectious Disease Diagnostics Laboratory, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shaon Sengupta
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Carolina B. López
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
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2
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Babawale PI, Guerrero-Plata A. Respiratory Viral Coinfections: Insights into Epidemiology, Immune Response, Pathology, and Clinical Outcomes. Pathogens 2024; 13:316. [PMID: 38668271 PMCID: PMC11053695 DOI: 10.3390/pathogens13040316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
Respiratory viral coinfections are a global public health threat that poses an economic burden on individuals, families, and healthcare infrastructure. Viruses may coinfect and interact synergistically or antagonistically, or their coinfection may not affect their replication rate. These interactions are specific to different virus combinations, which underlines the importance of understanding the mechanisms behind these differential viral interactions and the need for novel diagnostic methods to accurately identify multiple viruses causing a disease in a patient to avoid misdiagnosis. This review examines epidemiological patterns, pathology manifestations, and the immune response modulation of different respiratory viral combinations that occur during coinfections using different experimental models to better understand the dynamics respiratory viral coinfection takes in driving disease outcomes and severity, which is crucial to guide the development of prevention and treatment strategies.
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Affiliation(s)
| | - Antonieta Guerrero-Plata
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
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3
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Ono T, Hashimoto K, Kume Y, Chishiki M, Okabe H, Sato M, Norito S, Aso J, Sada M, Mochizuki I, Mashiyama F, Ishibashi N, Suzuki S, Sakuma H, Suwa R, Kawase M, Takeda M, Shirato K, Kimura H, Hosoya M. Molecular Diversity of Human Respiratory Syncytial Virus before and during the COVID-19 Pandemic in Two Neighboring Japanese Cities. Microbiol Spectr 2023; 11:e0260622. [PMID: 37409937 PMCID: PMC10433803 DOI: 10.1128/spectrum.02606-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Human respiratory syncytial viruses (HRSVs) are divided into subgroups A and B, which are further divided based on the nucleotide sequence of the second hypervariable region (HVR) of the attachment glycoprotein (G) gene. Understanding the molecular diversity of HRSV before and during the coronavirus disease 2019 (COVID-19) pandemic can provide insights into the effects of the pandemic on HRSV dissemination and guide vaccine development. Here, we analyzed HRSVs isolated in Fukushima Prefecture from September 2017 to December 2021. Specimens from pediatric patients were collected at two medical institutions in neighboring cities. A phylogenetic tree based on the second HVR nucleotide sequences was constructed using the Bayesian Markov chain Monte Carlo method. HRSV-A (ON1 genotype) and HRSV-B (BA9 genotype) were detected in 183 and 108 specimens, respectively. There were differences in the number of HRSV strains within clusters prevalent at the same time between the two hospitals. The genetic characteristics of HRSVs in 2021 after the COVID-19 outbreak were similar to those in 2019. HRSVs within a cluster may circulate within a region for several years, causing an epidemic cycle. Our findings add to the existing knowledge of the molecular epidemiology of HRSV in Japan. IMPORTANCE Understanding the molecular diversity of human respiratory syncytial viruses during pandemics caused by different viruses can provide insights that can guide public health decisions and vaccine development.
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Affiliation(s)
- Takashi Ono
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Yohei Kume
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Masatoki Sato
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Jumpei Aso
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Mitsuru Sada
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Izumi Mochizuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Fumi Mashiyama
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Fukushima, Japan
| | - Naohisa Ishibashi
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Shigeo Suzuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Hiroko Sakuma
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Fukushima, Japan
| | - Reiko Suwa
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Miyuki Kawase
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Takeda
- Department of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuya Shirato
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Gunma Paz University, Graduate School of Health Sciences, Takasaki, Gunma, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
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4
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Kim HN, Hwang J, Yoon SY, Lim CS, Cho Y, Lee CK, Nam MH. Molecular characterization of human respiratory syncytial virus in Seoul, South Korea, during 10 consecutive years, 2010-2019. PLoS One 2023; 18:e0283873. [PMID: 37023101 PMCID: PMC10079039 DOI: 10.1371/journal.pone.0283873] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/19/2023] [Indexed: 04/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections and hospitalization in infants and young children. Here, we analyzed the genetic diversity of RSV using partial G gene sequences in 84 RSV-A and 78 RSV- B positive samples collected in Seoul, South Korea, for 10 consecutive years, from 2010 to 2019. Our phylogenetic analysis revealed that RSV-A strains were classified into either the ON1 (80.9%) or NA1 (19.0%) genotypes. On the other hand, RSV-B strains demonstrated diversified clusters within the BA genotype. Notably, some sequences designated as BA-SE, BA-SE1, and BA-DIS did not cluster with previously identified BA genotypes in the phylogenetic trees. Despite this, they did not meet the criteria for the assignment of a new genotype based on recent classification methods. Selection pressure analysis identified three positive selection sites (amino acid positions 273, 274, and 298) in RSV-A, and one possible positive selection site (amino acid position 296) in RSV-B, respectively. The mean evolutionary rates of Korean RSV-A from 1999 to 2019 and RSV-B strains from 1991 and 2019 were estimated at 3.51 × 10-3 nucleotides (nt) substitutions/site/year and 3.32 × 10-3 nt substitutions/site/year, respectively. The population dynamics in the Bayesian skyline plot revealed fluctuations corresponding to the emergence of dominant strains, including a switch of the dominant genotype from NA1 to ON1. Our study on time-scaled cumulative evolutionary analysis contributes to a better understanding of RSV epidemiology at the local level in South Korea.
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Affiliation(s)
- Ha Nui Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Jinha Hwang
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Soo-Young Yoon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chang-Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
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5
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A Candidate Therapeutic Monoclonal Antibody Inhibits Both HRSV and HMPV Replication in Mice. Biomedicines 2022; 10:biomedicines10102516. [PMID: 36289776 PMCID: PMC9599547 DOI: 10.3390/biomedicines10102516] [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: 09/12/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
Human metapneumovirus (HMPV) and human respiratory virus (HRSV) are two leading causes of acute respiratory tract infection in young children. While there is no licensed drug against HMPV, the monoclonal antibody (mAb) Palivizumab is approved against HRSV for prophylaxis use only. Novel therapeutics against both viruses are therefore needed. Here, we describe the identification of human mAbs targeting these viruses by using flow cytometry-based cell sorting. One hundred and two antibodies were initially identified from flow cytometry-based cell sorting as binding to the fusion protein from HRSV, HMPV or both. Of those, 95 were successfully produced in plants, purified and characterized for binding activity by ELISA and neutralization assays as well as by inhibition of virus replication in mice. Twenty-two highly reactive mAbs targeting either HRSV or HMPV were isolated. Of these, three mAbs inhibited replication in vivo of a single virus while one mAb could reduce both HRSV and HMPV titers in the lung. Overall, this study identifies several human mAbs with virus-specific therapeutic potential and a unique mAb with inhibitory activities against both HRSV and HMPV.
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6
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Liu Z, Wu S, Xian Y, Gu Z, Liu W, Chen D, Zhou R. Seroprevalence of neutralizing antibodies against respiratory syncytial virus in healthy adults in Guangzhou, southern China. J Med Virol 2022; 94:4378-4382. [PMID: 35474462 DOI: 10.1002/jmv.27815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/07/2022] [Accepted: 04/24/2022] [Indexed: 11/10/2022]
Abstract
Respiratory syncytial virus (RSV) is the major cause of pneumonia and bronchiolitis in infants and young children, and mediates substantial morbidity and mortality in the elderly and immunocompromised globally. Development a safe and effective RSV vaccine and an optimized neutralizing antibody (NAb) with strong virus-neutralizing activity is appealing. To gain some detailed knowledge on the humoral immune response to RSV subgroup A (RSV-A) and RSV-B, we investigated the seroprevalence of pre-existing NAbs by using the microneutralization assay in healthy adult from Guangzhou, southern China. We found that the overall seropositive rate was 84.86% for anti-RSV NAbs. Furthermore, the seropositive rates were 68.47% and 73.61% for anti-RSV-A NAbs and anti-RSV-B NAbs, respectively. In addition, although the seropositive rates and NAb levels were not associated with the blood type, type AB individuals displaying higher seropositive rates for anti-RSV-A NAbs with high titer (≥ 288) and anti-RSV-B NAbs, especially those with moderate titer (≥ 72-< 288). The seropositive rates and titers were comparable between anti-RSV-A NAbs and anti-RSV-B NAbs in the AB blood type group. Interestingly, only when the NAb titer of the serum to RSV-A was not less than 288, was it not less than 18 to RSV-B, and vice versa. These results would be helpful for a better understanding of the human serum NAb responses to RSV-A and RSV-B. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zhenwei Liu
- State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China.,Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shangzhi Wu
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuting Xian
- State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zihao Gu
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Dehui Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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7
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Chen J, Qiu X, Avadhanula V, Shepard SS, Kim DK, Hixson J, Piedra PA, Bahl J. Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis. Influenza Other Respir Viruses 2021; 16:492-500. [PMID: 34894077 PMCID: PMC8983899 DOI: 10.1111/irv.12936] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/12/2021] [Accepted: 10/17/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition. METHODS We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances. RESULTS In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored. CONCLUSIONS This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.
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Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Xueting Qiu
- Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Do-Kyun Kim
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - James Hixson
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
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8
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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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9
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 DOI: 10.1002/jmv.v92.410.1002/jmv.25674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 05/24/2023]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019-nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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10
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 PMCID: PMC7166954 DOI: 10.1002/jmv.25674] [Citation(s) in RCA: 272] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 12/20/2022]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019‐nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray‐based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections. Respiratory tract viral infection including 2019‐nCoV poses great threats worldwide. Currently available and novel emerging diagnostic methods are summarized for several common respiratory viruses, including influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. This review is aimed to assist researchers and clinicians to develop timely and effective diagnostic strategies to detect respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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11
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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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12
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Ruzin A, Pastula ST, Levin-Sparenberg E, Jiang X, Fryzek J, Tovchigrechko A, Lu B, Qi Y, Liu H, Jin H, Yu L, Hackett J, Villafana T, Esser MT. Characterization of circulating RSV strains among subjects in the OUTSMART-RSV surveillance program during the 2016-17 winter viral season in the United States. PLoS One 2018; 13:e0200319. [PMID: 30040837 PMCID: PMC6057637 DOI: 10.1371/journal.pone.0200319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/22/2018] [Indexed: 01/10/2023] Open
Abstract
Background Respiratory syncytial virus (RSV) is an established cause of serious lower respiratory disease in infants, elderly and high-risk populations. The OUTSMART surveillance program aims to characterize patient populations and currently circulating RSV strains, and monitor temporal and geographic evolution of RSV F and G proteins in the U.S. Methods The OUTSMART 2016–17 study collected RSV-positive samples from 25 RSVAlert® laboratories from 4 U.S. regions and Puerto Rico during November 2016 through March 2017. Frequencies of A and B subtypes and genotypes were determined for several demographic and geographic variables. To gauge the representativeness of the OUTSMART patients, results were compared to discharge data from the NEDS and NIS databases. Results A total of 1,041 RSV-positive samples with associated demographic data were obtained and the RSV F gene and second variable region of the G gene were sequenced. The majority of samples (76.0%) came from children under 2 years old: <1 year (48.4%), 1–2 years (27.6%). The OUTSMART patient sample was similar to NEDS and NIS for age, gender, and geographic location. Both OUTSMART and national RSV cases peaked in January. Of OUTSMART samples, 45.3% were subtype A, 53.7% were subtype B and 1.0% were mixed A and B. The percentage of RSV B cases increased with increasing age. Hospitalization (length of hospital stay, LOS, >24 hrs) occurred in 29.0% of patients of which 52.0% had RSV B. Outpatients (LOS <24 hrs) were 64.4% of total of which 73.3% were diagnosed in the ER and discharged, while only 6% were diagnosed in other outpatient settings. Conclusions The OUTSMART 2016–17 study was representative of the U.S. RSV experience. Geographic and temporal information from the RSV surveillance program will be used to establish a molecular baseline of RSV F and G sequence variability and to help inform development of novel agents for RSV prophylaxis and treatment.
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Affiliation(s)
- Alexey Ruzin
- AstraZeneca/MedImmune, Gaithersburg, Maryland, United States of America
- * E-mail:
| | - Susan T. Pastula
- Epidstat Institute, Ann Arbor, Michigan, United States of America
| | | | - Xiaohui Jiang
- Epidstat Institute, Ann Arbor, Michigan, United States of America
| | - Jon Fryzek
- Epidstat Institute, Ann Arbor, Michigan, United States of America
| | | | - Bin Lu
- AstraZeneca/MedImmune, Mountain View, California, United States of America
| | - Yanping Qi
- AstraZeneca/MedImmune, Mountain View, California, United States of America
| | - Hui Liu
- AstraZeneca/MedImmune, Mountain View, California, United States of America
| | - Hong Jin
- AstraZeneca/MedImmune, Mountain View, California, United States of America
| | - Li Yu
- AstraZeneca/MedImmune, Gaithersburg, Maryland, United States of America
| | - Judith Hackett
- AstraZeneca/MedImmune, Gaithersburg, Maryland, United States of America
| | - Tonya Villafana
- AstraZeneca/MedImmune, Gaithersburg, Maryland, United States of America
| | - Mark T. Esser
- AstraZeneca/MedImmune, Gaithersburg, Maryland, United States of America
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13
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Complete Genome Sequence of an ON1 Human Respiratory Syncytial Virus Strain Isolated in Lebanon in 2015. GENOME ANNOUNCEMENTS 2018; 6:6/16/e00316-18. [PMID: 29674556 PMCID: PMC5908921 DOI: 10.1128/genomea.00316-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report here the complete genome sequence of a human respiratory syncytial virus (HRSV) strain obtained from an infant who presented to the emergency room with an acute respiratory illness during the 2014/2015 HRSV season in Lebanon. Analysis revealed that this virus belongs to the ON1 genotype that has recently emerged worldwide.
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14
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Abdel-Moneim AS, Soliman MS, Kamel MM, El-Kholy AA. Sequence analysis of the G gene of hRSVA ON1 genotype from Egyptian children with acute respiratory tract infections. J Med Microbiol 2018; 67:387-391. [PMID: 29458556 DOI: 10.1099/jmm.0.000699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human respiratory syncytial virus causes severe lower respiratory tract infection in neonates and children. Genotype ON1, with duplication of 72-nt in the G gene, was first detected in Canada and then recorded in other countries. In the current study, we describe the first detection of the ON1 genotype among children in Egypt in 2014/2015. Sequence analysis of the full-attachment G gene revealed that the majority of the strains examined were related to the ON1 genotype and only one sample related to N1 genotype. The Egyptian ON1 strains showed unique non-silent mutations in addition to variable mutations near the antigenic sites in comparison to the original ON1 ancestor strain. Continuous surveillance of hRSV regionally and globally is needed to understand the evolutionary mechanisms and strategies adopted by hRSV and their inducers for better adaption to the host.
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Affiliation(s)
- Ahmed S Abdel-Moneim
- Microbiology Department, College of Medicine, Taif University, Al-Taif 21944, Saudi Arabia.,Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt
| | - May S Soliman
- Clinical Pathology Department, College of Medicine, Cairo University, Giza, Egypt
| | - Mahmoud M Kamel
- Clinical Pathology Department, National Cancer Institute, Cairo University, Giza, Egypt
| | - Amani A El-Kholy
- Clinical Pathology Department, College of Medicine, Cairo University, Giza, Egypt
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15
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Pangesti KNA, Abd El Ghany M, Walsh MG, Kesson AM, Hill-Cawthorne GA. Molecular epidemiology of respiratory syncytial virus. Rev Med Virol 2018; 28. [PMID: 29377415 DOI: 10.1002/rmv.1968] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 01/10/2023]
Abstract
Respiratory syncytial virus (RSV) is a major cause of viral acute respiratory tract infections in young children. The virus is characterised by distinct seasonality that is dependent upon the latitude and its ability to cause reinfection. Respiratory syncytial virus demonstrates a complex molecular epidemiology pattern as multiple strains and/or genotypes cocirculate during a single epidemic. Previous studies have investigated the relationship between RSV genetic diversity, reinfection, and clinical features. Here, we review the evidence behind this relationship together with the impact that the advancement of whole genome sequencing will have upon our understanding and the need for reconsidering the classification of RSV genotypes.
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Affiliation(s)
| | - Moataz Abd El Ghany
- Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Michael G Walsh
- Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Alison M Kesson
- Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, Sydney, Australia.,Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia
| | - Grant A Hill-Cawthorne
- School of Public Health, The University of Sydney, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
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16
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Bayrakdar F, Kocabas CN, Altas AB, Kavuncuoglu HG, Cosgun Y, Mısırlıoglu ED, Durmaz I, Korukluoglu G, Ozkul A. Genetic variability human respiratory syncytial virus subgroups A and B in Turkey during six successive epidemic seasons, 2009-2015. J Med Virol 2017; 90:456-463. [PMID: 29077212 PMCID: PMC7166824 DOI: 10.1002/jmv.24983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/12/2017] [Indexed: 01/10/2023]
Abstract
Human respiratory syncytial virus (HRSV) is most important viral respiratory pathogen of acute lower respiratory tract infections in infants and young children worldwide. The circulating pattern and genetic characteristics in the HRSV attachment glycoprotein gene were investigated in Turkey during six consecutive seasons from 2009 to 2015. HRSVA was dominant in the all epidemic seasons except 2011‐2012 season. Partial sequences of the HVR2 region of the G gene of 479 HRSVA and 135 HRSVB were obtained. Most Turkish strains belonged to NA1, ON1, and BA9, which were the predominant genotypes circulating worldwide. Although three novel genotypes, TR‐A, TR‐BA1, and TR‐BA2, were identified, they were not predominant. Clinical data were available for 69 HRSV‐positive patients who were monitored due to acute lower respiratory tract illness. There were no significant differences in the clinical diagnosis, hospitalization rates, laboratory findings and treatment observed between the HRSVA and HRSVB groups, and co‐infections in this study. The major population afflicted by HRSV infections included infants and children between 13 and 24 months of age. We detected that the CB1, GB5, and THB strains clustered in the same branch with a bootstrap value of 100%. CB‐B and BA12 strains clustered in the same branch with a bootstrap value of 65%. The BA11 genotype was clustered in the BA9 genotype in our study. The present study may contribute on the molecular epidemiology of HRSV in Turkey and provide data for HRSV strains circulating in local communities and other regions worldwide.
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Affiliation(s)
- Fatma Bayrakdar
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Can Naci Kocabas
- Pediatric Immunology and Allergy Unit, Faculty of Medicine, Mugla Sitki Koçman Universty, Muğla, Turkey
| | - Ayse Basak Altas
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - H Gokhan Kavuncuoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Yasemin Cosgun
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Emine Dibek Mısırlıoglu
- Department of Pediatric Allergy and Immunology, Ankara Children's Hematology Oncology Training and Research Hospital, Ankara, Turkey
| | - Ihsan Durmaz
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Aykut Ozkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey
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17
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Levitz R, Gao Y, Dozmorov I, Song R, Wakeland EK, Kahn JS. Distinct patterns of innate immune activation by clinical isolates of respiratory syncytial virus. PLoS One 2017; 12:e0184318. [PMID: 28877226 PMCID: PMC5587315 DOI: 10.1371/journal.pone.0184318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/22/2017] [Indexed: 11/25/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major respiratory pathogen of infants and young children. Multiple strains of both subgroup A and B viruses circulate during each seasonal epidemic. Genetic heterogeneity among RSV genomes, in large part due to the error prone RNA-dependent, RNA polymerase, could mediate variations in pathogenicity. We evaluated clinical strains of RSV for their ability to induce the innate immune response. Subgroup B viruses were used to infect human pulmonary epithelial cells (A549) and primary monocyte-derived human macrophages (MDM) from a variety of donors. Secretions of IL-6 and CCL5 (RANTES) from infected cells were measured following infection. Host and viral transcriptome expression were assessed using RNA-SEQ technology and the genomic sequences of several clinical isolates were determined. There were dramatic differences in the induction of IL-6 and CCL5 in both A549 cells and MDM infected with a variety of clinical isolates of RSV. Transcriptome analyses revealed that the pattern of innate immune activation in MDM was virus-specific and host-specific. Specifically, viruses that induced high levels of secreted IL-6 and CCL5 tended to induce cellular innate immune pathways whereas viruses that induced relatively low level of IL-6 or CCL5 did not induce or suppressed innate immune gene expression. Activation of the host innate immune response mapped to variations in the RSV G gene and the M2-1 gene. Viral transcriptome data indicated that there was a gradient of transcription across the RSV genome though in some strains, RSV G was the expressed in the highest amounts at late times post-infection. Clinical strains of RSV differ in cytokine/chemokine induction and in induction and suppression of host genes expression suggesting that these viruses may have inherent differences in virulence potential. Identification of the genetic elements responsible for these differences may lead to novel approaches to antiviral agents and vaccines.
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Affiliation(s)
- Ruth Levitz
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yajing Gao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jeffrey S. Kahn
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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18
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Blais N, Gagné M, Hamuro Y, Rheault P, Boyer M, Steff AM, Baudoux G, Dewar V, Demers J, Ruelle JL, Martin D. Characterization of Pre-F-GCN4t, a Modified Human Respiratory Syncytial Virus Fusion Protein Stabilized in a Noncleaved Prefusion Conformation. J Virol 2017; 91:e02437-16. [PMID: 28404847 PMCID: PMC5469252 DOI: 10.1128/jvi.02437-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/04/2017] [Indexed: 12/20/2022] Open
Abstract
The human respiratory syncytial virus (hRSV) fusion (F) protein is considered a major target of the neutralizing antibody response to hRSV. This glycoprotein undergoes a major structural shift from the prefusion (pre-F) to the postfusion (post-F) state at the time of virus-host cell membrane fusion. Recent evidences suggest that the pre-F state is a superior target for neutralizing antibodies compared to the post-F state. Therefore, for vaccine purposes, we have designed and characterized a recombinant hRSV F protein, called Pre-F-GCN4t, stabilized in a pre-F conformation. To show that Pre-F-GCN4t does not switch to a post-F conformation, it was compared with a recombinant post-F molecule, called Post-F-XC. Pre-F-GCN4t was glycosylated and trimeric and displayed a conformational stability different from that of Post-F-XC, as shown by chemical denaturation. Electron microscopy analysis suggested that Pre-F-GCN4t adopts a lollipop-like structure. In contrast, Post-F-XC had a typical elongated conical shape. Hydrogen/deuterium exchange mass spectrometry demonstrated that the two molecules had common rigid folding core and dynamic regions and provided structural insight for their biophysical and biochemical properties and reactivity. Pre-F-GCN4t was shown to deplete hRSV-neutralizing antibodies from human serum more efficiently than Post-F-XC. Importantly, Pre-F-GCN4t was also shown to bind D25, a highly potent monoclonal antibody specific for the pre-F conformation. In conclusion, this construct presents several pre-F characteristics, does not switch to the post-F conformation, and presents antigenic features required for a protective neutralizing antibody response. Therefore, Pre-F-GCN4t can be considered a promising candidate vaccine antigen.IMPORTANCE Human respiratory syncytial virus (RSV) is a global leading cause of infant mortality and adult morbidity. The development of a safe and efficacious RSV vaccine remains an important goal. The RSV class I fusion (F) glycoprotein is considered one of the most promising vaccine candidates, and recent evidences suggest that the prefusion (pre-F) state is a superior target for neutralizing antibodies. Our study presents the physicochemical characterization of Pre-F-GCN4t, a molecule designed to be stabilized in the pre-F conformation. To confirm its pre-F conformation, Pre-F-GCN4t was analyzed in parallel with Post-F-XC, a molecule in the post-F conformation. Our results show that Pre-F-GCN4t presents characteristics of a stabilized pre-F conformation and support its use as an RSV vaccine antigen. Such an antigen may represent a significant advance in the development of an RSV vaccine.
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19
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Smith RJ, Hogan AB, Mercer GN. Unexpected Infection Spikes in a Model of Respiratory Syncytial Virus Vaccination. Vaccines (Basel) 2017; 5:E12. [PMID: 28524109 PMCID: PMC5492009 DOI: 10.3390/vaccines5020012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/06/2017] [Accepted: 05/15/2017] [Indexed: 12/04/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) is an acute respiratory infection that infects millions of children and infants worldwide. Recent research has shown promise for the development of a vaccine, with a range of vaccine types now in clinical trials or preclinical development. We extend an existing mathematical model with seasonal transmission to include vaccination. We model vaccination both as a continuous process, applying the vaccine during pregnancy, and as a discrete one, using impulsive differential equations, applying pulse vaccination. We develop conditions for the stability of the disease-free equilibrium and show that this equilibrium can be destabilised under certain extreme conditions, even with 100% coverage using an (unrealistic) vaccine. Using impulsive differential equations and introducing a new quantity, the impulsive reproduction number, we showed that eradication could be acheived with 75% coverage, while 50% coverage resulted in low-level oscillations. A vaccine that targets RSV infection has the potential to significantly reduce the overall prevalence of the disease, but appropriate coverage is critical.
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Affiliation(s)
- Robert J Smith
- Department of Mathematics and Faculty of Medicine, The University of Ottawa, 585 King Edward Ave, Ottawa, ON K1N 6N5, Canada.
| | - Alexandra B Hogan
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London W2 1PG, UK and Research School of Population Health, The Australian National University, Canberra 2601, Australia.
| | - Geoffry N Mercer
- Research School of Population Health, The Australian National University, Canberra 2601, Australia.
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20
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Moreira FB, Rosario CS, Santos JS, Avanzi VM, Nogueira MB, Vidal LR, Raboni SM. Molecular characterization and clinical epidemiology of human respiratory syncytial virus (HRSV) A and B in hospitalized children, Southern Brazil. J Med Virol 2017; 89:1489-1493. [PMID: 28213974 DOI: 10.1002/jmv.24795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/22/2017] [Indexed: 01/01/2023]
Abstract
Human respiratory syncytial virus (HRSV) is a major etiologic agent of pediatric respiratory infections. Genetic variability of its glycoprotein G enables HRSV to evade the immune response and determines its seasonal dissemination. This study reports genetic variability and clinical profiles of HRSV-infected patients from Southern Brazil. Seventy positive samples, 78% type A and 22% type B, were analyzed. Of the patients (median age, 6 months; interquartile range, 2-11 years), 16% had co-morbidities and 17% developed severe disease. The ON1 HRSV genotype first appeared in 2012, and patients infected with this genotype showed an increased tendency to develop severe disease.
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Affiliation(s)
- Francielli B Moreira
- Postgraduate Program in Microbiology, Parasitology and Pathology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Cristine S Rosario
- Department of Pediatrics, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Jucelia S Santos
- Postgraduate Program in Internal Medicine and Health Science, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Valéria M Avanzi
- Postgraduate Program in Internal Medicine and Health Science, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Meri Bordignon Nogueira
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Luine R Vidal
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Sonia Mara Raboni
- Postgraduate Program in Microbiology, Parasitology and Pathology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.,Postgraduate Program in Internal Medicine and Health Science, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.,Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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21
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Development of TaqMan RT-qPCR for the detection of type A human respiratory syncytial virus. Mol Cell Probes 2017; 33:16-19. [PMID: 28223170 DOI: 10.1016/j.mcp.2017.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/10/2017] [Accepted: 02/17/2017] [Indexed: 12/26/2022]
Abstract
The human respiratory syncytial virus is a common respiratory pathogen in children. Improved diagnosis of the virus is dependent on the development of tools for the rapid detection and estimation of the viral loads. In the current study, RT-qPCR using TaqMan hydrolysis probe based on the F gene detection was developed to identify and quantify hRSV in clinical samples. The assay was validated by comparing the results with a commercially available RT-qPCR kit. The newly developed assay was sensitive in detecting hRSV positive samples (59/126) which were equivalent to those detected by the commercial kit (57/126) with a detection limit of 1 × 102 copies/mL. A high correlation was found between the results of the newly developed assay and the commercial one. It was concluded that the newly developed RT-qPCR assay can be used as a sensitive detection tool for hRSV-A.
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22
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Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR. J Clin Virol 2017; 88:21-25. [PMID: 28107671 PMCID: PMC5331890 DOI: 10.1016/j.jcv.2016.12.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/20/2016] [Accepted: 12/31/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. OBJECTIVES Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. STUDY DESIGN Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples. Primer and probe binding regions in N gene were checked for mismatches and phylogenetic analyses done to determine molecular epidemiology of these viruses. New primers and probe were designed and tested on the previously real-time RT-PCR negative samples. RESULTS N gene sequences revealed 3 different mismatches in the probe target site of PCR negative, IFAT positive viruses. The primers target sites had no mismatches. Phylogenetic analysis of N and G genes showed that real-time RT-PCR positive and negative samples fell into distinct clades. Newly designed primers-probe pair improved detection and recovered previous PCR undetectable viruses. CONCLUSIONS An emerging RSV-B variant is undetectable by a quite widely used real-time RT-PCR assay due to polymorphisms that influence probe hybridization affecting PCR accuracy.
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23
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Bashir U, Nisar N, Mahmood N, Alam MM, Sadia H, Zaidi SSZ. Molecular detection and characterization of respiratory syncytial virus B genotypes circulating in Pakistani children. INFECTION GENETICS AND EVOLUTION 2016; 47:125-131. [PMID: 27908797 DOI: 10.1016/j.meegid.2016.11.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 10/20/2022]
Abstract
Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infections in young children, but very little is known about its epidemiology and circulating genotypes in Pakistan. This study analyzed the epidemiological and molecular characteristics of RSV B genotypes in Pakistani children below 5years with acute respiratory tract infections (ARIs) during three consecutive winter seasons from 2010 to 2013. A total of 1941 samples were analyzed for RSV infection by real time PCR and 24% (472/1941) samples were found positive out of which 22.3% (105/472) were sub-typed as RSV-B. The frequency of outpatient cases was higher (62.5%; 295/472) as compared to hospitalized patients (37.5%; 177/472). Patient ages ranged from 2month to 5years with a mean age of 1.48±1.2 (years) and a median age of 1year. Children below one year made up the highest percentage of enrolled subjects and male to female ratio of RSVB positive cases was nearly equivalent (1:1.1). The most common clinical symptoms were cough (96%), fever (80%) and sore throat (50%). All Pak RSVB strains ascribed to the BA genotype showing 91.9-97.1% and 86.2-95.3% homology at the nucleotide and amino acid levels respectively in comparison to BA prototype strain. On phylogenetic analysis, three genotypes of Pakistan RSV B viruses were observed; BA-9 and BA-10 which have been reported previously from other regions, and a third novel genotype assigned as BA-13 which formed a distinct cluster with protein length of 319 AA and showed 9-11 unique AA substitutions. All the RSV B isolates had two potential N-glycosylation sites in HVR2 of G protein and with heavy O-glycosylation of serine and threonine residues (G scores of 0.5-0.7). This study highlights the diversity of RSVB viruses and the significance of RSV as a dominant viral etiologic agent of pediatric ARI. It also emphasizes the need for continued molecular surveillance for early detection of prevalent and newly emerging genotypes to understand epidemiology of RSV infections in various regions of Pakistan.
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Affiliation(s)
- Uzma Bashir
- Atta-Ur-Rahman School of Applied Sciences, National University of Sciences and Technology, Islamabad, Pakistan; Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Nadia Nisar
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Nayab Mahmood
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Muhammad Masroor Alam
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan
| | - Hajra Sadia
- Atta-Ur-Rahman School of Applied Sciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
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24
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Liu W, Chen D, Tan W, Xu D, Qiu S, Zeng Z, Li X, Zhou R. Epidemiology and Clinical Presentations of Respiratory Syncytial Virus Subgroups A and B Detected with Multiplex Real-Time PCR. PLoS One 2016; 11:e0165108. [PMID: 27764220 PMCID: PMC5072546 DOI: 10.1371/journal.pone.0165108] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/06/2016] [Indexed: 01/29/2023] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most important pathogenic infections of children and requires in-depth research worldwide, and especially in developing countries. We used a novel multiplex real-time PCR to test 5483 patients (≤ 14 years old) hospitalized with respiratory illness in Guangzhou, China, over a 3-year period. Of these patients, 729 were positive for RSV-A (51.2%, 373/729) or RSV-B (48.8%, 356/729), but none was infected with both viruses. Two seasonal peaks in total RSV were detected at the changes from winter to spring and from summer to autumn. RSV-B was dominant in 2013 and RSV-A in 2015, whereas RSV-A and RSV-B cocirculated in 2014. The clinical presentations of 645 RSV-positive patients were analyzed. Bronchiolitis, dyspnea, coryza, vomiting, poor appetite, and diarrhea occurred more frequently in RSV-A-positive than RSV-B-positive patients, whereas chill, headache, myalgia, debility, and rash etc. were more frequent in RSV-B-positive than RSV-A-positive patients, suggesting specific clinical characteristics for RSV-A and RSV-B. Coinfectons with other pathogens were common and diverse. Bronchiolitis, fever (≥ 38°C), and poor appetite were more frequent in patients with single RSV infections than in coinfected patients, suggesting the key pathogenic activity of RSV. Analysis of the relationships between the comparative viral load and clinical presentations showed significant differences in bronchiolitis, fever (≥ 38°C), and rash etc. among patients with different viral loads. This study provides a novel rapid method for detecting RSV subgroups, and provides new insights into the epidemiology and clinical implications of RSV.
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Affiliation(s)
- Wenkuan Liu
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dehui Chen
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Weiping Tan
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Duo Xu
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shuyan Qiu
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhiqi Zeng
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao Li
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
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25
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Lam TTY, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annu Rev Genomics Hum Genet 2016; 17:193-218. [PMID: 27216777 DOI: 10.1146/annurev-genom-083115-022628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
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Affiliation(s)
- Tommy T-Y Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia;
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26
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Hu P, Zheng T, Chen J, Zhou T, Chen Y, Xu X, Pei X. Alternate circulation and genetic variation of human respiratory syncytial virus genotypes in Chengdu, West China, 2009-2014. J Med Virol 2016; 89:32-40. [PMID: 27322084 DOI: 10.1002/jmv.24603] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2016] [Indexed: 11/05/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a major pathogen that causes worldwide seasonal epidemic disease in infants due to its genetic variations. However, published information on the molecular epidemiology of HRSV was never reported particularly in Chengdu of West China. During five consecutive seasons (from 2009 to 2014), 433 (23.7%) of 1827 samples from hospitalized patients were identified as HRSV positive. Epidemiological characteristics of HRSV revealed that subtype A viruses (62.7%) prevailed in the first three epidemic seasons and faded in the next two seasons, while subtype B viruses (37.3%) kept circulating in five epidemic periods. According to the phylogenetic analysis of glycoprotein (G) gene, five HRSV genotypes NA1, ON1, BA9, BA-C, and CB1 were found in Chengdu. The predominant circulating genotype changed from NA1 in the period of 2010-2012 to BA9 of 2013-2014. The newly emerging ON1 was first reported in West China in October 2013. The early genotypes BA-C and CB1 were replaced by the prevailing BA9 after the third epidemic peak. Genetic mutations in glycosylation sites of G protein were found in HRSV variants, suggesting the virus is able to escape the immune recognition and attack. This study elucidated the local HRSV epidemic was associated with the alternate circulation of multiple genotypes and with the change of glycosylation sites of G protein. J. Med. Virol. 89:32-40, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Pengwei Hu
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China.,Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Tianli Zheng
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Jiayi Chen
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Tao Zhou
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Yuhang Chen
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xin Xu
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xiaofang Pei
- Departmentof Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China.
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27
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Do LAH, Wilm A, van Doorn HR, Lam HM, Sim S, Sukumaran R, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Dac NAT, Trinh HN, Nguyen TTH, Binh BTL, Le K, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, Farrar J, de Jong M, Chen S, Nagarajan N, Bryant JE, Hibberd ML. Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution. J Gen Virol 2016; 96:3470-3483. [PMID: 26407694 DOI: 10.1099/jgv.0.000298] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children ,2 years of age. Little is known about RSV intra-host genetic diversity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive samples (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our samples, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites inG were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic diversity. We further identified hotspots and coldspots of intra-host genetic diversity in the RSV genome, some of which may highlight previously unknown regions of functional importance.
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Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Andreas Wilm
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ha Minh Lam
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Shuzhen Sim
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - Rashmi Sukumaran
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - Anh Tuan Tran
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Bach Hue Nguyen
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thi Thu Loan Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quynh Huong Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quoc Bao Vo
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | | | - Hong Nhien Trinh
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | | | - Bao Tinh Le Binh
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Khanh Le
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Minh Tien Nguyen
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Quang Tung Thai
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thanh Vu Vo
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | | | - Thi Kim Huyen Dang
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Ngoc Huong Cao
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Thu Van Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Lu Viet Ho
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Menno de Jong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Swaine Chen
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | | | - Juliet E Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Martin L Hibberd
- Genome Institute of Singapore, Genome Building, 138672 Singapore
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28
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Oladokun R, Muloiwa R, Hsiao NY, Valley-Omar Z, Nuttall J, Eley B. Clinical characterisation and phylogeny of respiratory syncytial virus infection in hospitalised children at Red Cross War Memorial Children's Hospital, Cape Town. BMC Infect Dis 2016; 16:236. [PMID: 27246848 PMCID: PMC4888648 DOI: 10.1186/s12879-016-1572-5] [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: 02/02/2016] [Accepted: 05/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children in both the community and hospital setting. METHODS The clinical presentation, patient and phylogenetic characteristicsof laboratory-confirmed cases of RSV, as well as risk factors for nosocomial infectionat Red Cross War Memorial Children's Hospital in Cape Town were analysed. A multiplex PCR assay that detects 7 respiratory viruses was used to identify RSV nucleic acid on respiratory specimens. RESULTS A total of 226 children were studied, ages ranging between 1 week and 92.5 months (median: 2.8 months, IQR: 1.3-6.3 months) and 51.8 % were males. The median duration of symptoms prior to diagnosis was 2 days (IQR: 1-4 days). Nosocomial infections wereidentified in 22 (9.7 %) children. There were pre-existing medical conditions in 113 (50.0 %) excluding HIV, most commonly prematurity (n = 58, 50.0 %) and congenital heart disease (n = 34, 29.3 %). The commonest presenting symptoms were cough (196, 86.7 %), difficulty in breathing (115, 50.9 %) and fever (91, 41.6 %).A case fatality rate of 0.9 % was recorded. RSV group A predominated (n = 181, 80.1 %) while group B accounted for only 45 (19.9 %) of the infections. The prevalent genotypes were NA1 (n = 127,70.1 %), ON1 (n = 45,24.9 %) and NA2 (n = 9,5.0 %) for group A while the only circulating RSV B genotype was BA4. There was no significant difference in the genotype distribution between the nosocomial and community-acquired RSV infections. Age ≥ 6 months was independently associated with nosocomial infection. CONCLUSIONS A large percentage of children with RSV infection had pre-existing conditions. Approximately one tenth of the infections were nosocomial with age 6 months or older being a risk factor. Though both RSV groups co-circulated during the season, group A was predominant and included the novel ON1 genotype. Continued surveillance is necessary to identify prevalent and newly emerging genotypes ahead of vaccine development and efficacy studies.
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Affiliation(s)
- Regina Oladokun
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa. .,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.
| | - Rudzani Muloiwa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Grootes Schuur Hospital, Cape Town, South Africa
| | - Ziyaad Valley-Omar
- Centre for Respiratory Diseases and Meningitis, Virology, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa.,Faculty of Health Sciences, Department of Clinical Laboratory Sciences Medical Virology, University of Cape Town, Cape Town, South Africa
| | - James Nuttall
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
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29
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Maifeld SV, Ro B, Mok H, Chu M, Yu L, Yamagata R, Leonardson T, Chio V, Parhy B, Park S, Carlson M, Machhi S, Ulbrandt N, Falsey AR, Walsh EE, Wang CK, Esser MT, Zuo F. Development of Electrochemiluminescent Serology Assays to Measure the Humoral Response to Antigens of Respiratory Syncytial Virus. PLoS One 2016; 11:e0153019. [PMID: 27070145 PMCID: PMC4829208 DOI: 10.1371/journal.pone.0153019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 03/22/2016] [Indexed: 01/12/2023] Open
Abstract
Sensitive and precise serology assays are needed to measure the humoral response to antigens of respiratory syncytial virus (RSV) following natural infection or vaccination. We developed and evaluated a collection of electrochemiluminescent (ECL) serology assays using four RSV antigens (F, N, Ga and Gb). To assess the merits of ECL technology, the four ECL serology assays were evaluated using a well-characterized "gold standard" panel of acute and convalescent serum samples from fifty-nine RSV-positive and thirty RSV-negative elderly subjects (≥65 years old). The combined results from the four ECL assays demonstrated good concordance to the "gold standard" diagnosis, reaching 95% diagnostic sensitivity and 100% diagnostic specificity. Additionally, a combination of ECL assays provided higher diagnostic sensitivity than a commercially available diagnostic ELISA or cell-based microneutralization assay. In summary, these data demonstrate the advantages of using ECL-based serology assays and highlight their use as a sensitive diagnostic approach to detect recent RSV infection in an elderly population.
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Affiliation(s)
- Sarah V. Maifeld
- Applied Immunology and Microbiology, MedImmune, Mountain View, California, United States of America
| | - Bodrey Ro
- Applied Immunology and Microbiology, MedImmune, Mountain View, California, United States of America
| | - Hoyin Mok
- Applied Immunology and Microbiology, MedImmune, Mountain View, California, United States of America
| | - Marla Chu
- Applied Immunology and Microbiology, MedImmune, Mountain View, California, United States of America
| | - Li Yu
- Non-clinical Biostatistics, MedImmune, Gaithersburg, Maryland, United States of America
| | - Ryan Yamagata
- Non-clinical Biostatistics, MedImmune, Gaithersburg, Maryland, United States of America
| | - Tansy Leonardson
- Vaccine and Analytical Sciences, MedImmune, Mountain View, California, United States of America
| | - Vera Chio
- Vaccine and Analytical Sciences, MedImmune, Mountain View, California, United States of America
| | - Bandita Parhy
- Applied Immunology and Microbiology, MedImmune, Mountain View, California, United States of America
| | - Samuel Park
- Vaccine and Analytical Sciences, MedImmune, Mountain View, California, United States of America
| | - Marcia Carlson
- Purification Process Sciences, MedImmune, Gaithersburg, Maryland, United States of America
| | - Shushil Machhi
- Cell Culture and Fermentation Sciences, MedImmune, Gaithersburg, Maryland, United States of America
| | - Nancy Ulbrandt
- Department of Infectious Disease and Vaccines, Gaithersburg, California, United States of America
| | - Ann R. Falsey
- Department of Medicine, University of Rochester School of Medicine and Dentistry, and Department of Medicine, Rochester General Hospital, Rochester, New York, United States of America
| | - Edward E. Walsh
- Department of Medicine, University of Rochester School of Medicine and Dentistry, and Department of Medicine, Rochester General Hospital, Rochester, New York, United States of America
| | - C. Kathy Wang
- Applied Immunology and Microbiology, MedImmune, Mountain View, California, United States of America
| | - Mark T. Esser
- Translational Medicine, MedImmune, Gaithersburg, Maryland, United States of America
| | - Fengrong Zuo
- Applied Immunology and Microbiology, MedImmune, Mountain View, California, United States of America
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30
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Resch B, Kurath-Koller S, Eibisberger M, Zenz W. Prematurity and the burden of influenza and respiratory syncytial virus disease. World J Pediatr 2016; 12:8-18. [PMID: 26582294 DOI: 10.1007/s12519-015-0055-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/11/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND Respiratory morbidity of former preterm infants and especially those with bronchopulmonary dysplasia (BPD) is high during infancy and early childhood. DATA SOURCES We performed a review based on a literature search including EMBASE, MEDLINE, and CINAHL databases to identify all relevant papers published in the English and German literature on influenza and respiratory syncytial virus infection associated with preterm infant, prematurity, and BPD between 1980 and 2014. RESULTS Recurrent respiratory symptoms remain common at preschool age, school age and even into young adulthood. Acute viral respiratory tract infections due to different pathogens cause significant morbidity and necessitate rehospitalizations during the first years of life. Influenza virus infection plays a minor role compared to respiratory syncytial virus (RSV) associated respiratory tract infection during infancy and early childhood. Nevertheless, particular morbidity to both viruses is high. CONCLUSIONS The particular burden of both viral diseases in preterm infants is dominated by RSV and its associated rehospitalizations during the first two years of life. Prophylactic measures include vaccination against influenza virus of family members and caregivers and active immunization starting at the age of 6 months, and monthly injections of palivizumab during the cold season to avoid severe RSV disease and its sequelae.
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Affiliation(s)
- Bernhard Resch
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Division of Neonatology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria.
| | - Stefan Kurath-Koller
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria
| | - Monika Eibisberger
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Austria
| | - Werner Zenz
- Research Unit for Infectious Diseases and Vaccinology, Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
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31
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Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. J Virol 2015; 89:3444-54. [PMID: 25609811 PMCID: PMC4403408 DOI: 10.1128/jvi.03391-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is associated with severe childhood respiratory infections. A clear description of local RSV molecular epidemiology, evolution, and transmission requires detailed sequence data and can inform new strategies for virus control and vaccine development. We have generated 27 complete or nearly complete genomes of RSV from hospitalized children attending a rural coastal district hospital in Kilifi, Kenya, over a 10-year period using a novel full-genome deep-sequencing process. Phylogenetic analysis of the new genomes demonstrated the existence and cocirculation of multiple genotypes in both RSV A and B groups in Kilifi. Comparison of local versus global strains demonstrated that most RSV A variants observed locally in Kilifi were also seen in other parts of the world, while the Kilifi RSV B genomes encoded a high degree of variation that was not observed in other parts of the world. The nucleotide substitution rates for the individual open reading frames (ORFs) were highest in the regions encoding the attachment (G) glycoprotein and the NS2 protein. The analysis of RSV full genomes, compared to subgenomic regions, provided more precise estimates of the RSV sequence changes and revealed important patterns of RSV genomic variation and global movement. The novel sequencing method and the new RSV genomic sequences reported here expand our knowledge base for large-scale RSV epidemiological and transmission studies. IMPORTANCE The new RSV genomic sequences and the novel sequencing method reported here provide important data for understanding RSV transmission and vaccine development. Given the complex interplay between RSV A and RSV B infections, the existence of local RSV B evolution is an important factor in vaccine deployment.
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32
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Recombinant subgroup B human respiratory syncytial virus expressing enhanced green fluorescent protein efficiently replicates in primary human cells and is virulent in cotton rats. J Virol 2014; 89:2849-56. [PMID: 25540371 DOI: 10.1128/jvi.03587-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Human respiratory syncytial virus (HRSV) is the most important viral cause of severe respiratory tract disease in infants. Two subgroups (A and B) have been identified, which cocirculate during, or alternate between, yearly epidemics and cause indistinguishable disease. Existing in vitro and in vivo models of HRSV focus almost exclusively on subgroup A viruses. Here, a recombinant (r) subgroup B virus (rHRSV(B05)) was generated based on a consensus genome sequence obtained directly from an unpassaged clinical specimen from a hospitalized infant. An additional transcription unit containing the gene encoding enhanced green fluorescent protein (EGFP) was introduced between the phosphoprotein and matrix genes (position 5) of the genome to generate rHRSV(B05)EGFP(5). The recombinant viruses replicated efficiently in both HEp-2 cells and in well-differentiated normal human bronchial cells grown at air-liquid interface. Intranasal infection of cotton rats (Sigmodon hispidus) resulted in high numbers of EGFP(+) cells in epithelia of the nasal septum and conchae. When administered in a relatively large inoculum volume, the virus also replicated efficiently in bronchiolar epithelial cells and spread extensively in both the upper and lower respiratory tracts. Virus replication was not observed in ciliated epithelial cells of the trachea. This is the first virulent rHRSV strain with the genetic composition of a currently circulating wild-type virus. In vivo tracking of infected cells by means of EGFP fluorescence in the absence of cytopathic changes increases the sensitivity of virus detection in HRSV pathogenesis studies. IMPORTANCE Virology as a discipline has depended on monitoring cytopathic effects following virus culture in vitro. However, wild-type viruses isolated from patients often do not cause significant changes to infected cells, necessitating blind passage. This can lead to genetic and phenotypic changes and the generation of high-titer, laboratory-adapted viruses with diminished virulence in animal models of disease. To address this, we determined the genome sequence of an unpassaged human respiratory syncytial virus from a sample obtained directly from an infected infant, assembled a molecular clone, and recovered a wild-type recombinant virus. Addition of a gene encoding enhanced green fluorescent protein allowed this wild-type virus to be tracked in primary human cells and living animals in the absence of significant cytopathic effects. Imaging of fluorescent cells proved to be a highly valuable tool for monitoring the spread of virus and may help improve assays for evaluating novel intervention strategies.
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Abstract
Acute respiratory tract infection (RTI) is a leading cause of morbidity and mortality worldwide and the majority of RTIs are caused by viruses, among which respiratory syncytial virus (RSV) and the closely related human metapneumovirus (hMPV) figure prominently. Host innate immune response has been implicated in recognition, protection and immune pathological mechanisms. Host-viral interactions are generally initiated via host recognition of pathogen-associated molecular patterns (PAMPs) of the virus. This recognition occurs through host pattern recognition receptors (PRRs) which are expressed on innate immune cells such as epithelial cells, dendritic cells, macrophages and neutrophils. Multiple PRR families, including Toll-like receptors (TLRs), RIG-I-like receptors (RLRs) and NOD-like receptors (NLRs), contribute significantly to viral detection, leading to induction of cytokines, chemokines and type I interferons (IFNs), which subsequently facilitate the eradication of the virus. This review focuses on the current literature on RSV and hMPV infection and the role of PRRs in establishing/mediating the infection in both in vitro and in vivo models. A better understanding of the complex interplay between these two viruses and host PRRs might lead to efficient prophylactic and therapeutic treatments, as well as the development of adequate vaccines.
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Raghunandan R, Lu H, Zhou B, Xabier MG, Massare MJ, Flyer DC, Fries LF, Smith GE, Glenn GM. An insect cell derived respiratory syncytial virus (RSV) F nanoparticle vaccine induces antigenic site II antibodies and protects against RSV challenge in cotton rats by active and passive immunization. Vaccine 2014; 32:6485-92. [PMID: 25269094 PMCID: PMC7172787 DOI: 10.1016/j.vaccine.2014.09.030] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/12/2014] [Accepted: 09/14/2014] [Indexed: 12/02/2022]
Abstract
Post-infectious immunity to respiratory syncytial virus (RSV) infection results in limited protection as evidenced by the high rate of infant hospitalization in the face of high titer, maternally derived RSV-specific antibodies. By contrast, RSV fusion (F) glycoprotein antigenic site II humanized monoclonal antibodies, palivizumab and motavizumab, have been shown to reduce RSV-related hospitalization in infants. Immunogenicity and efficacy studies were conducted in cotton rats comparing a recombinant RSV F nanoparticle vaccine with palivizumab and controlled with live RSV virus intranasal immunization and, formalin inactivated RSV vaccine. Active immunization with RSV F nanoparticle vaccine containing an alum adjuvant induced serum levels of palivizumab competing antibody (PCA) greater than passive administration of 15 mg/kg palivizumab (human prophylactic dose) in cotton rats and neutralized RSV-A and RSV-B viruses. Immunization prevented detectable RSV replication in the lungs and, unlike passive administration of palivizumab, in the nasal passage of challenged cotton rats. Histology of lung tissues following RSV challenge showed no enhanced disease in the vaccinated groups in contrast to formalin inactivated 'Lot 100' vaccine. Passive intramuscular administration of RSV F vaccine-induced immune sera one day prior to challenge of cotton rats reduced viral titers by 2 or more log10 virus per gram of lung and nasal tissue and at doses less than palivizumab. A recombinant RSV F nanoparticle vaccine protected lower and upper respiratory tract against both RSV A and B strain infection and induced polyclonal palivizumab competing antibodies similar to but potentially more broadly protective against RSV than palivizumab.
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Affiliation(s)
- Rama Raghunandan
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States.
| | - Hanxin Lu
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States
| | - Bin Zhou
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States
| | | | - Michael J Massare
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States
| | - David C Flyer
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States
| | - Louis F Fries
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States
| | - Gale E Smith
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States
| | - Gregory M Glenn
- Novavax Inc., 20 Firstfield Road, Gaithersburg MD 20878, United States
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Martinelli M, Frati ER, Zappa A, Ebranati E, Bianchi S, Pariani E, Amendola A, Zehender G, Tanzi E. Phylogeny and population dynamics of respiratory syncytial virus (Rsv) A and B. Virus Res 2014; 189:293-302. [PMID: 24954788 DOI: 10.1016/j.virusres.2014.06.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/06/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
Abstract
Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in infants and young children. RSV is characterised by high variability, especially in the G glycoprotein, which may play a significant role in RSV pathogenicity by allowing immune evasion. To reconstruct the origin and phylodynamic history of RSV, we evaluated the genetic diversity and evolutionary dynamics of RSV A and RSV B isolated from children under 3 years old infected in Italy from 2006 to 2012. Phylogenetic analysis revealed that most of the RSV A sequences clustered with the NA1 genotype, and RSV B sequences were included in the Buenos Aires genotype. The mean evolutionary rates for RSV A and RSV B were estimated to be 2.1 × 10(-3) substitutions (subs)/site/year and 3.03 × 10(-3) subs/site/year, respectively. The time of most recent common ancestor for the tree root went back to the 1940s (95% highest posterior density-HPD: 1927-1951) for RSV A and the 1950s (95%HPD: 1951-1960) for RSV B. The RSV A Bayesian skyline plot (BSP) showed a decrease in transmission events ending in about 2005, when a sharp growth restored the original viral population size. RSV B BSP showed a similar trend. Site-specific selection analysis identified 10 codons under positive selection in RSV A sequences and only one site in RSV B sequences. Although RSV remains difficult to control due to its antigenic diversity, it is important to monitor changes in its coding sequences, to permit the identification of future epidemic strains and to implement vaccine and therapy strategies.
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Affiliation(s)
- Marianna Martinelli
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133, Milan, Italy.
| | - Elena Rosanna Frati
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133, Milan, Italy.
| | - Alessandra Zappa
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133, Milan, Italy.
| | - Erika Ebranati
- "L. Sacco" Department of Biomedical and Clinical Sciences, University of Milan, Via G. B. Grassi 74, 20157 Milano, Italy.
| | - Silvia Bianchi
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133, Milan, Italy.
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133, Milan, Italy; CIRI-IT, Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy.
| | - Antonella Amendola
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133, Milan, Italy; CIRI-IT, Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy.
| | - Gianguglielmo Zehender
- "L. Sacco" Department of Biomedical and Clinical Sciences, University of Milan, Via G. B. Grassi 74, 20157 Milano, Italy.
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133, Milan, Italy; CIRI-IT, Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy.
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Kim YJ, Kim DW, Lee WJ, Yun MR, Lee HY, Lee HS, Jung HD, Kim K. Rapid replacement of human respiratory syncytial virus A with the ON1 genotype having 72 nucleotide duplication in G gene. INFECTION GENETICS AND EVOLUTION 2014; 26:103-12. [PMID: 24820343 PMCID: PMC7106136 DOI: 10.1016/j.meegid.2014.05.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/23/2014] [Accepted: 05/05/2014] [Indexed: 02/01/2023]
Abstract
We investigated the prevalence of HRSV during 2008–2013. Novel HRSV-A ON1 genotype was emerged in August 2011. After 1 year of emergence in 2012–2013, 94.6% was replaced with novel ON1 genotype. Evolutionary dynamics also drastically increased in 2011. The result of epitope prediction shows the possibilities of antigenic variation.
Human respiratory syncytial virus (HRSV) is the main cause of severe respiratory illness in young children and elderly people. We investigated the genetic characteristics of the circulating HRSV subgroup A (HRSV-A) to determine the distribution of genotype ON1, which has a 72-nucleotide duplication in attachment G gene. We obtained 456 HRSV-A positive samples between October 2008 and February 2013, which were subjected to sequence analysis. The first ON1 genotype was discovered in August 2011 and 273 samples were identified as ON1 up to February 2013. The prevalence of the ON1 genotype increased rapidly from 17.4% in 2011–2012 to 94.6% in 2012–2013. The mean evolutionary rate of G protein was calculated as 3.275 × 10−3 nucleotide substitution/site/year and several positively selected sites for amino acid substitutions were located in the predicted epitope region. This basic and important information may facilitate a better understanding of HRSV epidemiology and evolution.
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Affiliation(s)
- You-Jin Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Dae-Won Kim
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Wan-Ji Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Mi-Ran Yun
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Ho Yeon Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Han Saem Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Hee-Dong Jung
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Kisoon Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea.
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Robinson MJ, Tan CS, Fenwick F, Chambers CJ, Routledge EG, Toms GL. Generation and epitope mapping of a sub-group cross-reactive anti-respiratory syncytial virus G glycoprotein monoclonal antibody which is protective in vivo. J Med Virol 2014; 86:1267-77. [PMID: 24415460 DOI: 10.1002/jmv.23881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2013] [Indexed: 11/07/2022]
Abstract
Passively administered antibodies to conserved epitopes on the attachment (G) glycoprotein of human respiratory syncytial virus (hRSV) have potential in the immunoprophylaxis of human infections. This study set out to generate monoclonal antibodies (MAbs) recognizing all prevalent lineages of HRSV and capable of immunoprophylaxis in mice. Two murine MAbs of broad specificity for prevalent virus strains were generated by immunization of mice with hRSV of sub-group A followed by selection of hybridomas on recombinant G glycoprotein from a sub-group B virus. The anti-G hybridomas generated secreted antibody of high affinity but negligible neutralizing capacity one of which was tested in mice and found to be protective against live virus challenge. Western blotting and partial epitope mapping on transiently expressed G-glycoprotein fragments indicate that these antibodies recognize a complex epitope on the protein backbone of the molecule involving residues both C'- and N-terminal to the central conserved motif.
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Affiliation(s)
- Mark J Robinson
- Institute of Cellular Medicine, The Medical School, Newcastle upon Tyne, United Kingdom
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Almajhdi FN, Farrag MA, Amer HM. Group B strains of human respiratory syncytial virus in Saudi Arabia: molecular and phylogenetic analysis. Virus Genes 2013; 48:252-9. [PMID: 24370974 DOI: 10.1007/s11262-013-1030-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 12/19/2013] [Indexed: 11/28/2022]
Abstract
The genetic variability and circulation pattern of human respiratory syncytial virus group B (HRSV-B) strains, identified in Riyadh during the winters of 2008 and 2009, were evaluated by partial sequencing of the attachment (G) protein gene. The second hypervariable region (HVR-2) of G gene was amplified by RT-PCR, sequenced and compared to representatives of different HRSV-B genotypes. Sequence and phylogenetic analysis revealed that all Saudi strains belonged to the genotype BA, which is characterized by 60-nucleotide duplication at HVR-2. Only strains of 2008 were clustered with subgroup BA-IV, while those isolated at 2009 were clustered among the most recent subgroups (particularly BA-X and CB-B). Amino acid sequence analysis demonstrated 18 amino acid substitutions in Saudi HRSV-B strains; among which five are specific for individual strains. Furthermore, two potential N-glycosylation sites at residues 230 and 296 were identified for all Saudi strains, and an additional site at amino acid 273 was found only in Riyadh 28/2008 strain. O-glycosylation was predicted in 42-43 sites, where the majority (no = 38) are highly conserved among Saudi strains. The average ratio between non-synonymous and synonymous mutations (ω) implied stabilizing selection pressure on G protein, with evidences of positive selection on certain Saudi strains. This report provides preliminary data on the circulation pattern and molecular characteristics of HRSV-B strains circulating in Saudi Arabia.
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Affiliation(s)
- Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia,
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Priestnall SL, Mitchell JA, Walker CA, Erles K, Brownlie J. New and Emerging Pathogens in Canine Infectious Respiratory Disease. Vet Pathol 2013; 51:492-504. [DOI: 10.1177/0300985813511130] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Canine infectious respiratory disease is a common, worldwide disease syndrome of multifactorial etiology. This review presents a summary of 6 viruses (canine respiratory coronavirus, canine pneumovirus, canine influenza virus, pantropic canine coronavirus, canine bocavirus, and canine hepacivirus) and 2 bacteria ( Streptococcus zooepidemicus and Mycoplasma cynos) that have been associated with respiratory disease in dogs. For some pathogens a causal role is clear, whereas for others, ongoing research aims to uncover their pathogenesis and contribution to this complex syndrome. Etiology, clinical disease, pathogenesis, and epidemiology are described for each pathogen, with an emphasis on recent discoveries or novel findings.
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Affiliation(s)
- S. L. Priestnall
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, Hertfordshire, UK
| | - J. A. Mitchell
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, Hertfordshire, UK
| | - C. A. Walker
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, Hertfordshire, UK
| | - K. Erles
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, Hertfordshire, UK
| | - J. Brownlie
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, Hertfordshire, UK
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Aamir UB, Alam MM, Sadia H, Zaidi SSZ, Kazi BM. Molecular characterization of circulating respiratory syncytial virus (RSV) genotypes in Gilgit Baltistan Province of Pakistan during 2011-2012 winter season. PLoS One 2013; 8:e74018. [PMID: 24058513 PMCID: PMC3772930 DOI: 10.1371/journal.pone.0074018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/25/2013] [Indexed: 11/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infections in young children, but very little is known about its epidemiology and circulating genotypes in Pakistan. This study analyzed the epidemiological and molecular characteristics of RSV genotypes detected in Pakistani children less than 2 years of age with acute respiratory tract infections (ARIs) in a tertiary care hospital in Gilgit Baltistan (GB) province during 2011-12 winter season. RSV was detected in 75 out of 105 children presenting with acute respiratory infection. Male infants between 2-6 months age made up the highest percentage of RSV positive cases. Epidemiological factors such as pre-maturity, mean weight, clinical features and diagnosis when compared between RSV positive and negative groups were found to be statistically insignificant. Phylogenetic analysis classified all 75 of the RSV strains into 71 strains of subgroups A and 4 strains of subgroup B, respectively. Strains belonging to subgroups A and B were further subdivided into NA1/GA2 and BA, respectively. The nucleotide and deduced amino acid sequence identities were relatively high among these strains (>90%). Both RSV-A and RSV-B isolates had two potential N-glycosylation sites in HVR2 of G protein and with heavy O-glycosylation of serine and threonine residues (G scores of 0.5-0.7). This report highlights the significance of RSV as a dominant viral etiologic agent of pediatric ARIs, and need for continued molecular epidemiological surveys for early detection of prevalent strains and newly emerging genotypes to understand epidemiology of RSV infections in various regions of Pakistan.
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Affiliation(s)
- Uzma Bashir Aamir
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, Pakistan
| | - Muhammad Masroor Alam
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, Pakistan
| | - Hajra Sadia
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, Pakistan
- * E-mail:
| | - Birjees Mazher Kazi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, Pakistan
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Almajhdi FN, Farrag MA, Amer HM. Genetic diversity in the G protein gene of group A human respiratory syncytial viruses circulating in Riyadh, Saudi Arabia. Arch Virol 2013; 159:73-81. [PMID: 23884633 DOI: 10.1007/s00705-013-1792-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/07/2013] [Indexed: 11/26/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a frequent cause of hospitalization and mortality in children worldwide. The molecular epidemiology and circulation pattern of HRSV in Saudi Arabia is mostly uncharted. In the current study, the genetic variability and phylogenetic relationships of HRSV type A strains circulating in Riyadh Province were explored. Nasopharyngeal aspirates were collected from hospitalized children with acute respiratory symptoms during the winter-spring seasons of 2007/08 and 2008/09. Among 175 samples analyzed, 39 (22.3 %) were positive for HRSV by one-step RT-PCR (59 % type A and 41 % type B). Propagation of positive samples in HEp-2 cells permitted the recovery of the first Saudi HRSV isolates. Genetic variability among Saudi HRSV-A strains was evaluated by sequence analysis of the complete attachment (G) protein gene. The nucleotide sequence was compared to representatives of the previously identified HRSV-A genotypes. Sequence and phylogenetic analysis showed that the strains examined in this study were very closely related at both the nucleotide and amino acid level, and all of them are clustered in the GA2 genotype (and mostly belonged to the NA-1 subtype). A total of 23 mutation sites, 14 of which resulted in an amino acid change, were recorded only in Saudi strains. This is the first report on genetic diversity of HRSV-A strains in Saudi Arabia. Further analysis of strains on a geographical and temporal basis is needed to fully understand HRSV-A circulation patterns in Saudi Arabia.
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Affiliation(s)
- Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia,
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Should respiratory care in preterm infants include prophylaxis against respiratory syncytial virus infection? The case in favour. Paediatr Respir Rev 2013; 14:130-6. [PMID: 23375547 DOI: 10.1016/j.prrv.2012.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Respiratory syncytial virus (RSV) is the most significant cause of acute respiratory tract infections (RTI) in infants and young children throughout the world. Preterm infants are at increased risk for severe RSV lower respiratory tract infection due to small lung volumes, a reduced lung surface area, small airways and an increased air space wall thickness. Additionally, the airways of preterm infants have been ventilated mechanically and suctioned and potentially damaged by many microtraumas with disruption of endothelial surfaces enabling pathogens to invade more easily. The immune system of preterm infants is immature resulting in low antibody titers (incomplete transplacental transfer of maternal antibodies) and a reduced cellular immunity with reduced viral clearance. Rehospitalization rates of preterm compared to term infants due to RSV infection are increased as are total morbidity and mortality associated with RSV disease. Palivizumab effectively reduces RSV related rehospitalisation in this high-risk population.
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Molecular epidemiology and phylodynamics of the human respiratory syncytial virus fusion protein in northern Taiwan. PLoS One 2013; 8:e64012. [PMID: 23734183 PMCID: PMC3667090 DOI: 10.1371/journal.pone.0064012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/08/2013] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND AND AIMS The glycoprotein (G protein) and fusion protein (F protein) of respiratory syncytial virus (RSV) both show genetic variability, but few studies have examined the F protein gene. This study aimed to characterize the molecular epidemiology and phylodynamics of the F protein gene in clinical RSV strains isolated in northern Taiwan from 2000-2011. METHODS RSV isolates from children presenting with acute respiratory symptoms between July 2000 and June 2011 were typed based on F protein gene sequences. Phylogeny construction and evaluation were performed using the neighbor-joining (NJ) and maximum likelihood (ML) methods. Phylodynamic patterns in RSV F protein genes were analyzed using the Bayesian Markov Chain Monte Carlo framework. Selection pressure on the F protein gene was detected using the Datamonkey website interface. RESULTS From a total of 325 clinical RSV strains studied, phylogenetic analysis showed that 83 subgroup A strains (RSV-A) could be further divided into three clusters, whereas 58 subgroup B strains (RSV-B) had no significant clustering. Three amino acids were observed to differ between RSV-A and -B (positions 111, 113, and 114) in CTL HLA-B*57- and HLA-A*01-restricted epitopes. One positive selection site was observed in RSV-B, while none was observed in RSV-A. The evolution rate of the virus had very little change before 2000, then slowed down between 2000 and 2005, and evolved significantly faster after 2005. The dominant subtypes of RSV-A in each epidemic were replaced by different subtypes in the subsequent epidemic. CONCLUSIONS Before 2004, RSV-A infections were involved in several small epidemics and only very limited numbers of strains evolved and re-emerged in subsequent years. After 2005, the circulating RSV-A strains were different from those of the previous years and continued evolving through 2010. Phylodynamic pattern showed the evolutionary divergence of RSV increased significantly in the recent 5 years in northern Taiwan.
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Moura FEA, Perdigão ACB, Ribeiro JF, Florêncio CMGD, Oliveira FMS, Pereira SAR, Botosso VF, Siqueira MM, Thomazelli LM, Caldeira RN, Oliveira DBL, Durigon EL. Respiratory syncytial virus epidemic periods in an equatorial city of Brazil. Influenza Other Respir Viruses 2013; 7:1128-35. [PMID: 23517375 PMCID: PMC4634240 DOI: 10.1111/irv.12104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2013] [Indexed: 11/28/2022] Open
Abstract
Background Characterization of the human respiratory syncytial virus (HRSV) season at the local level has important implications for appropriate decisions on the time period for administration of specific prophylaxis. Objectives (1) To describe five consecutive epidemic periods of HRSV in an equatorial city of Brazil and (2) to show preliminary data on genomic diversity of circulating HRSV. Patients/Methods Nasopharyngeal aspirates of 2885 children attending the emergency room and wards of a public hospital were collected and screened by indirect immunofluorescence for HRSV infections during five consecutive years (from January 2004 to December 2008). In addition, the genetic and antigenic variability of the HRSV strains isolated was evaluated by partial nucleotide sequencing of the protein G gene. Results HRSV was detected in 15·8% of the analyzed samples. HRSV seasons occurred in a restricted period of each year. The onset of each HRSV season was variable (February to May), but the end always occurred in July. From the 456 HRSV infections found, 86 cases with bronchiolitis were genotyped. Both HRSV subgroups (A and B) cocirculated during the five epidemic periods. The 58 HRSV‐A strains grouped into two clades, GA2 and GA5. In respect of the HRSV‐B strains, the 28 samples grouped into two clades: GB3 and BA. Conclusions HRSV accounts for a substantial proportion of ARI in the study population. As in temperate countries, HRSV infections in this equatorial area of Brazil also cause seasonal yearly epidemics, and this has implications for prophylaxis strategies. The city of Fortaleza follows the same worldwide trend of circulation of genotypes of HRSV.
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Qin X, Zhang C, Zhao Y, Zhao X. Genetic variability of subgroup A and B respiratory syncytial virus strains circulating in southwestern China from 2009 to 2011. Arch Virol 2013; 158:1487-95. [DOI: 10.1007/s00705-012-1552-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/14/2012] [Indexed: 11/30/2022]
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Kaaijk P, Luytjes W, Rots NY. Vaccination against RSV: is maternal vaccination a good alternative to other approaches? Hum Vaccin Immunother 2013; 9:1263-7. [PMID: 23442726 PMCID: PMC3901815 DOI: 10.4161/hv.24096] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The respiratory syncytial virus (RSV) is the major cause of lower respiratory tract illness (LRI) in infants worldwide. Also persons with heart/lung disease or an immunodeficiency disorder, and the elderly are at increased risk for severe LRI upon RSV infection. Although there is at present no licensed RSV vaccine available, it is a priority target for several vaccine developers. For the implementation of a future RSV vaccination within national immunization schemes, various strategies can be considered even without the availability of extended clinical data on RSV vaccines. For this purpose, the extensive knowledge on RSV with respect to disease pathology, epidemiology and immunology can be used. This article discusses different aspects that should be considered to enable a successful implementation of a new RSV vaccine in national immunization programs. In addition, gaps in knowledge that needs further attention are identified. The maternal immunization strategy is highlighted, but also vaccination in the youngest infants and specific risk group immunization strategies are evaluated in this paper. Key factors such as the seasonality of RSV disease, interference of maternal antibodies and the immaturity of the infants’ immune system are addressed.
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Affiliation(s)
- Patricia Kaaijk
- Centre for infectious Diseases Control; National Institute for Public Health and the Environment (RIVM); Bilthoven, the Netherlands
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Delayed RSV diagnosis in a stem cell transplant population due to mutations that result in negative polymerase chain reaction. Diagn Microbiol Infect Dis 2013; 75:426-30. [PMID: 23415542 DOI: 10.1016/j.diagmicrobio.2012.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/19/2012] [Accepted: 12/24/2012] [Indexed: 11/24/2022]
Abstract
Respiratory syncytial virus (RSV) is a serious cause of morbidity and mortality in the adult hematopoietic stem cell transplant (HSCT) population. The timely diagnosis of RSV infection in this population is important for initiating therapy and instituting appropriate infection prevention measures. Molecular multiplex assays now offer increased sensitivity for a more accurate diagnosis. This study presents 5 cases of RSV infection in HSCT patients in which diagnosis was delayed due to false-negative results from a multiplex polymerase chain reaction (PCR) assay. The false-negative result was due to a single base-pair mutation in the RSV strain. These false results delayed the appropriate treatment of patients. This study shows that a combination of a multiplex PCR assay, viral antigen, and/or culture should be used to detect variants of RSV in patients and that multiplex respiratory viral assays should develop a more robust design that includes multiple genetic target per virus to prevent missing viruses that continue to have genetic variances.
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Molecular epidemiology and disease severity of human respiratory syncytial virus in Vietnam. PLoS One 2013; 8:e45436. [PMID: 23349659 PMCID: PMC3551923 DOI: 10.1371/journal.pone.0045436] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/17/2012] [Indexed: 11/19/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of acute respiratory infections (ARIs) in children worldwide and can cause high mortality, especially in developing countries. However, information on the clinical and molecular characteristics of RSV infection in developing countries is limited. From April 2010 to May 2011, 1,082 nasopharyngeal swabs were collected from children with ARI admitted to the Children's Hospital 2, Ho Chi Minh City, Vietnam. Samples were screened for RSV and genotyped by reverse transcription-PCR and sequencing. Demographic and clinical data was also recorded. RSV was found in 23.8% (257/1,082) of samples. RSV A was the dominant subgroup, accounting for 91.4% (235/257), followed by RSV B, 5.1% (13/257), and 9 cases (3.5%) were mixed infection of these subgroups. The phylogenetic analysis revealed that all group A strains belonged to the GA2 genotype. All group B strains belonged to the recently identified BA genotype, and further clustered into 2 recently described subgenotypes BA9 and BA10. One GA2 genotype strain had a premature stop codon which shortened the G protein length. RSV infection was significantly associated with younger age and higher severity score than those without. Co-infection with other viruses did not affect disease severity. RSV A caused more severe disease than RSV B. The results from this study will not only contribute to the growing database on the molecular diversity of RSV circulating worldwide but may be also useful in clinical management and vaccine development.
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Balmaks R, Ribakova I, Gardovska D, Kazaks A. Molecular epidemiology of respiratory syncytial virus during the 2009–2010 season in Latvia. Arch Virol 2013; 158:1089-92. [DOI: 10.1007/s00705-012-1586-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/20/2012] [Indexed: 11/24/2022]
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Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology. PLoS One 2012; 7:e51439. [PMID: 23236501 PMCID: PMC3517519 DOI: 10.1371/journal.pone.0051439] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 10/31/2012] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is an important cause of severe lower respiratory tract infections in infants and the elderly. In the vast majority of cases, however, RSV infections run mild and symptoms resemble those of a common cold. The immunological, clinical, and epidemiological profile of severe RSV infections suggests a disease caused by a virus with typical seasonal transmission behavior, lacking clear-cut virulence factors, but instead causing disease by modifying the host’s immune response in a way that stimulates pathogenesis. Yet, the interplay between RSV-evoked immune responses and epidemic behavior, and how this affects the genomic evolutionary dynamics of the virus, remains poorly understood. Here, we present a comprehensive collection of 33 novel RSV subgroup A genomes from strains sampled over the last decade, and provide the first measurement of RSV-A genomic diversity through time in a phylodynamic framework. In addition, we map amino acid substitutions per protein to determine mutational hotspots in specific domains. Using Bayesian genealogical inference, we estimated the genomic evolutionary rate to be 6.47×10−4 (credible interval: 5.56×10−4, 7.38×10−4) substitutions/site/year, considerably slower than previous estimates based on G gene sequences only. The G gene is however marked by elevated substitution rates compared to other RSV genes, which can be attributed to relaxed selective constraints. In line with this, site-specific selection analyses identify the G gene as the major target of diversifying selection. Importantly, statistical analysis demonstrates that the immune driven positive selection does not leave a measurable imprint on the genome phylogeny, implying that RSV lineage replacement mainly follows nonselective epidemiological processes. The roughly 50 years of RSV-A genomic evolution are characterized by a constant population size through time and general co-circulation of lineages over many epidemic seasons – a conclusion that might be taken into account when developing future therapeutic and preventive strategies.
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