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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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Hönemann M, Thiem S, Bergs S, Berthold T, Propach C, Siekmeyer M, Frille A, Wallborn T, Maier M, Pietsch C. In-Depth Analysis of the Re-Emergence of Respiratory Syncytial Virus at a Tertiary Care Hospital in Germany in the Summer of 2021 after the Alleviation of Non-Pharmaceutical Interventions Due to the SARS-CoV-2 Pandemic. Viruses 2023; 15:v15040877. [PMID: 37112857 PMCID: PMC10144477 DOI: 10.3390/v15040877] [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: 02/24/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Following the extensive non-pharmaceutical interventions (NPIs) and behavioral changes in the wake of the SARS-CoV-2 pandemic, an interseasonal rise in respiratory syncytial virus (RSV) cases was observed in Germany in 2021. The aim of this study was to characterize the local molecular epidemiology of RSV infections in comparison to the three pre-pandemic seasons. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of RSV infections. RSV detections peaked in calendar week 40 of 2021, 18 weeks earlier than the usual peak observed in the three pre-pandemic seasons. Sequence analysis revealed a close phylogenetic relatedness regardless of the season of origin. A significantly higher amount of pediatric cases (88.9% of all cases, p < 0.001) was observed for season 2021/2022. For the pediatric cases, significant differences were observed for an increased number of siblings in the household (p = 0.004), a lower rate of fever (p = 0.007), and a reduced amount of co-infections (p = 0.001). Although the mean age of the adult patients was significantly younger (47.1 vs. 64.7, p < 0.001), high rates of comorbidities, lower respiratory tract infections and intensive care unit admissions prevailed. The NPIs in the wake of the SARS-CoV-2 pandemic had a tremendous impact on the epidemiologic characteristics and seasonality of RSV and warrant further epidemiologic studies of this important pathogen.
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Affiliation(s)
- Mario Hönemann
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Stephanie Thiem
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Sandra Bergs
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Tom Berthold
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Christian Propach
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Manuela Siekmeyer
- Department of Pediatrics, University of Leipzig, Liebigstrasse 20a, 04103 Leipzig, Germany
| | - Armin Frille
- Department of Respiratory Medicine, University of Leipzig, Liebigstrasse 20, 04103 Leipzig, Germany
| | - Tillmann Wallborn
- Department of Pediatrics, Klinikum St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany
| | - Melanie Maier
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
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Pre COVID-19 molecular epidemiology of respiratory syncytial virus (RSV) among children in Bangladesh. Heliyon 2022; 8:e11043. [PMID: 36247113 PMCID: PMC9551109 DOI: 10.1016/j.heliyon.2022.e11043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/24/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Epidemiological data of specific respiratory pathogens from the pre-COVID-19 period are essential to determine the effects of the COVID-19 pandemic on other respiratory infections. In this study, we revealed the pre-COVID-19 molecular epidemiology of respiratory syncytial virus (RSV) among children in Bangladesh. We tested 3170 samples collected from 2008 to 2012 for a panel of respiratory viruses; RSV, human metapneumovirus (hMPV), human parainfluenza viruses (hPIV) 1, 2, 3, and adenovirus. Five hundred fifty-five samples (17.5 %) were positive for RSV, including 2.5% having co-infections with other viruses. Genotypic characterization of RSV showed that RSV-A (82%) contributed more acute respiratory infections than RSV-B (18%). Clinical features were similar with RSV-A and RSV-B infections. However, children with RSV-B were more likely to have upper respiratory infections (URI) (10% vs. 29%, p = 0.03). Among RSV-A cases, hospitalization was higher for ON1 cases (25%, ON1 vs. 8%, NA1, p = 0.04), whereas the recovery without a disability was higher among the NA1 cases (56%, ON1 vs. 88%, NA1, p = 0.02). The time to the most recent common ancestor (TMRCA) for RSV in Bangladesh was 1949 for RSV-A and 1944 for RSV-B. This study revealed the genotypic diversity and evolutionary relatedness of RSV strains in Bangladesh and provided pre-COVID molecular epidemiology data to understand better the COVID-19 impact on upcoming RSV epidemiology in Bangladesh.
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Kafintu-Kwashie AA, Nii-Trebi NI, Obodai E, Neizer M, Adiku TK, Odoom JK. Molecular epidemiological surveillance of viral agents of acute lower respiratory tract infections in children in Accra, Ghana. BMC Pediatr 2022; 22:364. [PMID: 35751110 PMCID: PMC9229459 DOI: 10.1186/s12887-022-03419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute lower respiratory tract infection (ALRTI) in children under 5 years is known to be predominantly caused by respiratory syncytial virus (RSV). In recent times, however, human metapneumovirus (HMPV) has also been implicated. This study sought to investigate and genotype respiratory syncytial virus and human metapneumovirus in children presenting with ALRTIs infection at the Princess Marie Louis Children's Hospital in Accra, Ghana. METHODS Children below 5 years who were clinically diagnosed of ALRTI and on admission at the study site were recruited between September 2015 and November 2016 for this study. Demographic data information was obtained by means of a standardized questionnaire; and relevant clinical information was obtained from medical records. Nasopharyngeal swabs were collected from 176 children recruited for the study. Ribonucleic acid was extracted from swabs and cDNA syntheses were performed by RT-PCR. RSV-positive amplicons were sequenced and analyzed for genotype assignment. RESULTS RSV and HMPV prevalence among the sampled subjects were 11.4 and 1.7% respectively. Of the RSV positives, 8/20 (40%) were RSV-A and 12/20 (60%) were RSV-B. The highest prevalence was observed in children less than 12 months old. Phylogenetic analysis of the second hypervariable region of the RSV G-gene revealed that all RSV group A viruses belonged to the "novel" ON1 genotype containing the 72-nucleotide duplication; and RSV group B viruses belong to the BA IX genotype. CONCLUSION RSV is frequently detected in children aged under 5 years admitted with ALRTI in Ghana. Continued surveillance of viral aetiological agents is warranted to elucidate the prevalence and transmission patterns of viral pathogens that cause respiratory tract infections among children. This will help inform appropriate intervention approaches.
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Theophilus Korku Adiku
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - John Kofi Odoom
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
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Sun YP, Lei SY, Wang YB, Wang YZ, Qiang HS, Yin YF, Jiang ZM, Zhu M, Chen XL, Ye HM, Zheng ZZ, Xia NS. Molecular Evolution of Attachment Glycoprotein (G) and Fusion Protein (F) Genes of Respiratory Syncytial Virus ON1 and BA9 Strains in Xiamen, China. Microbiol Spectr 2022; 10:e0208321. [PMID: 35311585 PMCID: PMC9045328 DOI: 10.1128/spectrum.02083-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/23/2022] [Indexed: 11/20/2022] Open
Abstract
Monitoring viral transmission and analyzing the genetic diversity of a virus are imperative to better understand its evolutionary history and the mechanism driving its evolution and spread. Especially, effective monitoring of key antigenic mutations and immune escape variants caused by these mutations has great scientific importance. Thus, to further understand the molecular evolutionary dynamics of respiratory syncytial virus (RSV) circulating in China, we analyzed nasopharyngeal swab specimens derived from hospitalized children ≤5 years old with acute respiratory tract infections (ARIs) in Xiamen during 2016 to 2019. We found that infants under 6 months of age (52.0%) were the main population with RSV infection. The prevalent pattern "BBAA" of RSV was observed during the epidemic seasons. RSV ON1 and BA9 genotypes were the dominant circulating strains in Xiamen. Interestingly, we observed four Xiamen-specific amino acid substitution combinations in the G protein and several amino acid mutations primarily occurring at antigenic sites Ø and V in the F protein. Our analyses suggest that introduction of new viruses and local evolution are shaping the diversification of RSV strains in Xiamen. This study provides new insights on the evolution and spread of the ON1 and BA9 genotypes at local and global scales. IMPORTANCE Monitoring the amino acid diversity of the RSV G and F genes helps us to find the novel genotypes, key antigenic mutations affecting antigenicity, or neutralizing antibody-resistant variants produced by natural evolution. In this study, we analyzed the molecular evolution of G and F genes from RSV strains circulating in Xiamen, China. These data provide new insights on local and global transmission and could inform the development of control measures for RSV infections.
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Affiliation(s)
- Yong-Peng Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Si-Yu Lei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Ying-Bin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Yi-Zhen Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Hong-Sheng Qiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Yi-Fan Yin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Ze-Min Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Min Zhu
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiao-Li Chen
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Hui-Ming Ye
- Department of Clinical Laboratory, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Zi-Zheng Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Ning-Shao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, People’s Republic of China
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Wangui J, Nokes DJ, Mobegi VA, Otieno JR, Agoti CN, Ngeranwa JJN, Bulimo WD. Spatial-temporal distribution and sequence diversity of group a human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype. Influenza Other Respir Viruses 2021; 16:501-510. [PMID: 34962085 PMCID: PMC8983921 DOI: 10.1111/irv.12948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/05/2021] [Indexed: 12/02/2022] Open
Abstract
Background Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial–temporal distribution as defined by its genetic diversity. Methods A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT‐PCR (reverse transcriptase polymerase chain reaction). A segment of the G‐gene was amplified using one‐step RT‐PCR and sequenced by Sanger di‐deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction. Results Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%), and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi[π]) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes. Conclusions HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2, and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing toward the Western zones and decreasing toward the Eastern zones of the country.
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Affiliation(s)
- Julia Wangui
- Department of Biochemistry, Kenyatta University, Nairobi, Kenya.,Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - D James Nokes
- Department of Epidemiology and Demography, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Victor A Mobegi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - James R Otieno
- Department of Epidemiology and Demography, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.,Department of Epidemiology and Demography, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Wallace D Bulimo
- Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
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Korsun N, Angelova S, Trifonova I, Voleva S, Grigorova I, Tzotcheva I, Mileva S, Alexiev I, Perenovska P. Predominance of ON1 and BA9 genotypes of respiratory syncytial virus (RSV) in Bulgaria, 2016-2018. J Med Virol 2021; 93:3401-3411. [PMID: 32779756 DOI: 10.1002/jmv.26415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/07/2020] [Accepted: 08/06/2020] [Indexed: 11/06/2022]
Abstract
The objectives of this study were to investigate the prevalence of respiratory syncytial virus (RSV) infections in Bulgaria, to characterize the genetic diversity of the RSV strains, and to perform amino acid sequence analysis of the RSV G protein. Clinical, epidemiological data and nasopharyngeal swabs were prospectively collected from children aged less than 5 years presenting with acute respiratory infections from October 2016 to September 2018. Real-time polymerase chain reaction for 12 respiratory viruses, and sequencing, phylogenetic, and amino acid analyses of the RSV G gene/protein were performed. Of the 875 children examined, 645 (73.7%) were positive for at least one viral respiratory pathogen. RSV was the most commonly detected virus (26.2%), followed by rhinoviruses (15%), influenza A (H3N2) (9.7%), adenoviruses (9%), bocaviruses (7.2%), human metapneumovirus (6.1%), parainfluenza viruses 1/2/3 (5.8%), influenza type B (5.5%), and A(H1N1)pdm09 (3.4%). The detection rate for RSV varied across two winter seasons (36.7% vs 20.3%). RSV-B cases outnumbered those of the RSV-A throughout the study period. RSV was the most common virus detected in patients with bronchiolitis (45.1%) and pneumonia (24%). Phylogenetic analysis indicated that all the sequenced RSV-A strains belonged to the ON1 genotype and the RSV-B strains were classified as BA9 genotype. Amino acid substitutions at 15 and 22 positions of the HVR-2 were identified compared with the ON1 and BA prototype strains, respectively. This study revealed the leading role of RSV as a causative agent of serious respiratory illnesses in early childhood, year-on-year fluctuations in RSV incidence, the dominance of RSV-B, and relatively low genetic diversity in the circulating RSV strains.
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Affiliation(s)
- Neli Korsun
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Svetla Angelova
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivelina Trifonova
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Silvia Voleva
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iliana Grigorova
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iren Tzotcheva
- Pediatric Clinic, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
| | - Sirma Mileva
- Pediatric Clinic, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
| | - Ivaylo Alexiev
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Penka Perenovska
- Pediatric Clinic, University Hospital Alexandrovska, Medical University, Sofia, Bulgaria
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Respiratory syncytial virus B sequence analysis reveals a novel early genotype. Sci Rep 2021; 11:3452. [PMID: 33568737 PMCID: PMC7876121 DOI: 10.1038/s41598-021-83079-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.
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9
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任 康, 任 洛, 邓 昱, 谢 晓, 臧 娜, 谢 军, 罗 征, 罗 健, 符 州, 刘 恩, 李 渠. [Epidemiological characteristics of respiratory syncytial virus in hospitalized children with acute lower respiratory tract infection in Chongqing, China, from 2013 to 2018: an analysis of 2 066 cases]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:67-73. [PMID: 33476540 PMCID: PMC7818151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/18/2020] [Indexed: 11/11/2023]
Abstract
OBJECTIVE To study the detection rate, epidemic pattern, and clinical features of respiratory syncytial virus (RSV) in hospitalized children with acute lower respiratory infection (ALRI). METHODS Nasopharyngeal aspirates were collected from children with ALRI, aged < 2 years, who were hospitalized in Children's Hospital of Chongqing Medical University from June 2013 to May 2018. Multiplex PCR was used to detect 16 common respiratory viruses. The epidemiological characteristics of RSV were analyzed. RESULTS A total of 2 066 hospitalized children with ALRI were enrolled. Among the children, 1 595 (77.20%) tested positive for virus and 826 (39.98%) tested positive for RSV [410(49.6%) positive for RSV-A, 414 (50.1%) positive for RSV-B, and 2 (0.2%) positive for both RSV-A and RSV-B]. RSV-B was the main subtype detected in 2013-2014 and 2016-2017, while RSV-A was the main subtype in 2014-2015 and 2017-2018, and these two subtypes were prevalent in 2015-2016. The highest detection rate of RSV was noted in winter. RSV + human rhinovirus was the most common combination of viruses and was detected in 123 children. These children were more likely to develop wheezing than those with single RSV detected (P=0.030). A total of 298 samples were detected with single RSV, 148 were detected with RSV mixed with other viruses, 389 were detected with other viruses, and 241 were detected negative for viruses. Compared with the other viruses and negative virus groups, the single RSV group had a significantly younger age and significantly higher incidence rates of dyspnea, respiratory failure, and severe lower respiratory tract infection (P < 0.0083). The RSV-A positive group had a significantly higher proportion of boys than the RSV-B positive group (P=0.004), but there were no significant differences in clinical manifestations between the two groups. CONCLUSIONS In Chongqing in 2013-2018, RSV-A and RSV-B not only can predominate alternately, but also can co-circulate during a season. RSV is the major viral pathogen of hospitalized children with ALRI and can cause severe lower respiratory tract infection. There are no differences in clinical manifestations between children with RSV-A infection and those with RSV-B infection, but boys are more susceptible to RSV-A infection.
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Affiliation(s)
- 康轶 任
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 洛 任
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 昱 邓
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 晓虹 谢
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 娜 臧
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 军 谢
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 征秀 罗
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 健 罗
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 州 符
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 恩梅 刘
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 渠北 李
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
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任 康, 任 洛, 邓 昱, 谢 晓, 臧 娜, 谢 军, 罗 征, 罗 健, 符 州, 刘 恩, 李 渠. [Epidemiological characteristics of respiratory syncytial virus in hospitalized children with acute lower respiratory tract infection in Chongqing, China, from 2013 to 2018: an analysis of 2 066 cases]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:67-73. [PMID: 33476540 PMCID: PMC7818151 DOI: 10.7499/j.issn.1008-8830.2007139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVE To study the detection rate, epidemic pattern, and clinical features of respiratory syncytial virus (RSV) in hospitalized children with acute lower respiratory infection (ALRI). METHODS Nasopharyngeal aspirates were collected from children with ALRI, aged < 2 years, who were hospitalized in Children's Hospital of Chongqing Medical University from June 2013 to May 2018. Multiplex PCR was used to detect 16 common respiratory viruses. The epidemiological characteristics of RSV were analyzed. RESULTS A total of 2 066 hospitalized children with ALRI were enrolled. Among the children, 1 595 (77.20%) tested positive for virus and 826 (39.98%) tested positive for RSV [410(49.6%) positive for RSV-A, 414 (50.1%) positive for RSV-B, and 2 (0.2%) positive for both RSV-A and RSV-B]. RSV-B was the main subtype detected in 2013-2014 and 2016-2017, while RSV-A was the main subtype in 2014-2015 and 2017-2018, and these two subtypes were prevalent in 2015-2016. The highest detection rate of RSV was noted in winter. RSV + human rhinovirus was the most common combination of viruses and was detected in 123 children. These children were more likely to develop wheezing than those with single RSV detected (P=0.030). A total of 298 samples were detected with single RSV, 148 were detected with RSV mixed with other viruses, 389 were detected with other viruses, and 241 were detected negative for viruses. Compared with the other viruses and negative virus groups, the single RSV group had a significantly younger age and significantly higher incidence rates of dyspnea, respiratory failure, and severe lower respiratory tract infection (P < 0.0083). The RSV-A positive group had a significantly higher proportion of boys than the RSV-B positive group (P=0.004), but there were no significant differences in clinical manifestations between the two groups. CONCLUSIONS In Chongqing in 2013-2018, RSV-A and RSV-B not only can predominate alternately, but also can co-circulate during a season. RSV is the major viral pathogen of hospitalized children with ALRI and can cause severe lower respiratory tract infection. There are no differences in clinical manifestations between children with RSV-A infection and those with RSV-B infection, but boys are more susceptible to RSV-A infection.
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Affiliation(s)
- 康轶 任
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 洛 任
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 昱 邓
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 晓虹 谢
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 娜 臧
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 军 谢
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 征秀 罗
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 健 罗
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 州 符
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 恩梅 刘
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - 渠北 李
- />重庆医科大学附属儿童医院呼吸科/国家儿童健康与疾病临床医学研究中心/儿童发育疾病研究教育部重点实验室/儿童感染免疫重庆市重点实验室, 重庆 400014Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
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Ramaekers K, Rector A, Cuypers L, Lemey P, Keyaerts E, Van Ranst M. Towards a unified classification for human respiratory syncytial virus genotypes. Virus Evol 2020; 6:veaa052. [PMID: 33072402 PMCID: PMC7552823 DOI: 10.1093/ve/veaa052] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Since the first human respiratory syncytial virus (HRSV) genotype classification in 1998, inconsistent conclusions have been drawn regarding the criteria that define HRSV genotypes and their nomenclature, challenging data comparisons between research groups. In this study, we aim to unify the field of HRSV genotype classification by reviewing the different methods that have been used in the past to define HRSV genotypes and by proposing a new classification procedure, based on well-established phylogenetic methods. All available complete HRSV genomes (>12,000 bp) were downloaded from GenBank and divided into the two subgroups: HRSV-A and HRSV-B. From whole-genome alignments, the regions that correspond to the open reading frame of the glycoprotein G and the second hypervariable region (HVR2) of the ectodomain were extracted. In the resulting partial alignments, the phylogenetic signal within each fragment was assessed. Maximum likelihood phylogenetic trees were reconstructed using the complete genome alignments. Patristic distances were calculated between all pairs of tips in the phylogenetic tree and summarized as a density plot in order to determine a cutoff value at the lowest point following the major distance peak. Our data show that neither the HVR2 fragment nor the G gene contains sufficient phylogenetic signal to perform reliable phylogenetic reconstruction. Therefore, whole-genome alignments were used to determine HRSV genotypes. We define a genotype using the following criteria: a bootstrap support of ≥70 per cent for the respective clade and a maximum patristic distance between all members of the clade of ≤0.018 substitutions per site for HRSV-A or ≤0.026 substitutions per site for HRSV-B. By applying this definition, we distinguish twenty-three genotypes within subtype HRSV-A and six genotypes within subtype HRSV-B. Applying the genotype criteria on subsampled data sets confirmed the robustness of the method.
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Affiliation(s)
- Kaat Ramaekers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
| | - Annabel Rector
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
| | - Lize Cuypers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium.,University Hospitals Leuven, Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, Herestraat 49, BE-3000 Leuven, Belgium
| | - Philippe Lemey
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
| | - Els Keyaerts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium.,University Hospitals Leuven, Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, Herestraat 49, BE-3000 Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium.,University Hospitals Leuven, Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, Herestraat 49, BE-3000 Leuven, Belgium
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12
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Pangesti KNA, El Ghany MA, Kesson AM, Hill-Cawthorne GA. Respiratory syncytial virus in the Western Pacific Region: a systematic review and meta-analysis. J Glob Health 2020; 9:020431. [PMID: 31893034 PMCID: PMC6925967 DOI: 10.7189/jogh.09.020431] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is the leading cause of viral pneumonia and bronchiolitis, especially in younger children. The burden of RSV infection in adults, particularly in the older age group, is increasingly recognised. However, RSV disease burden and molecular epidemiology in the World Health Organization (WHO) Western Pacific Region (WPR) has not been reviewed systematically. The aim of this systematic review is to investigate the epidemiological aspects of RSV (incidence, prevalence, seasonality and hospitalisation status) and the associated molecular data in the WPRO countries. Methods A systematic search was conducted in international literature databases (MEDLINE, EMBASE, Scopus and Web of Science) to identify RSV-related publications from January 2000 to October 2017 in the WPR countries. Results A total of 196 studies from 15 WPR countries were included. The positivity rate for RSV among respiratory tract infection patients was 16.73% (95% confidence interval (CI) = 15.12%-18.4%). The RSV-positive cases were mostly found in hospitalised compared with outpatients (18.28% vs 11.54%, P < 0.001), and children compared with adults (20.72% vs 1.87%, P < 0.001). The seasonality of RSV in the WPR countries follows the latitude, with the peak of RSV season occurring in the winter in temperate countries, and during the rainy season in tropical countries. The molecular epidemiology pattern of RSV in WPR countries was similar to the global pattern, with NA1 (RSV A) and BA (RSV B) being the predominant genotypes. Conclusions The available data on RSV are limited in several countries within the WPR, with most data focusing on children and hospitalised patients. Further studies and surveillance, incorporating laboratory testing, are needed to determine the burden of RSV infection in the WPR countries.
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Affiliation(s)
- Krisna N A Pangesti
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Australia.,The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia.,Center for Research and Development of Biomedical and Basic Health Technology, NIHRD, Jakarta, Indonesia
| | - Moataz Abd El Ghany
- The 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.,The Westmead Clinical School, Faculty of Medicine and Health, 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.,The Children Hospital at Westmead, Department of Infectious Diseases and Microbiology, Sydney, Australia
| | - Grant A Hill-Cawthorne
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
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13
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Muñoz-Escalante JC, Comas-García A, Bernal-Silva S, Robles-Espinoza CD, Gómez-Leal G, Noyola DE. Respiratory syncytial virus A genotype classification based on systematic intergenotypic and intragenotypic sequence analysis. Sci Rep 2019; 9:20097. [PMID: 31882808 PMCID: PMC6934736 DOI: 10.1038/s41598-019-56552-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022] Open
Abstract
Respiratory syncytial virus (RSV), a leading cause of lower respiratory tract infections, is classified in two major groups (A and B) with multiple genotypes within them. Continuous changes in spatiotemporal distribution of RSV genotypes have been recorded since the identification of this virus. However, there are no established criteria for genotype definition, which affects the understanding of viral evolution, immunity, and development of vaccines. We conducted a phylogenetic analysis of 4,353 RSV-A G gene ectodomain sequences, and used 1,103 complete genome sequences to analyze the totallity of RSV-A genes. Intra- and intergenotype p-distance analysis and identification of molecular markers associated to specific genotypes were performed. Our results indicate that previously reported genotypes can be classified into nine distinct genotypes: GA1-GA7, SAA1, and NA1. We propose the analysis of the G gene ectodomain with a wide set of reference sequences of all genotypes for an accurate genotype identification.
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Affiliation(s)
- Juan Carlos Muñoz-Escalante
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Andreu Comas-García
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
- Center for Research in Biomedicine and Health Sciences, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Sofía Bernal-Silva
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
- Center for Research in Biomedicine and Health Sciences, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | | | - Guillermo Gómez-Leal
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Daniel E Noyola
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
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Isolation and Characterization of Clinical RSV Isolates in Belgium during the Winters of 2016-2018. Viruses 2019; 11:v11111031. [PMID: 31698728 PMCID: PMC6893609 DOI: 10.3390/v11111031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) is a very important viral pathogen in children, immunocompromised and cardiopulmonary diseased patients and the elderly. Most of the published research with RSV was performed on RSV Long and RSV A2, isolated in 1956 and 1961, yet recent RSV isolates differ from these prototype strains. Additionally, these viruses have been serially passaged in cell culture, which may result in adaptations that affect virus–host interactions. We have isolated RSV from mucosal secretions of 12 patients in the winters 2016–2017 and 2017–2018, of which eight RSV-A subtypes and four RSV-B subtypes. Passage 3 of the isolates was assessed for viral replication kinetics and infectious virus production in HEp-2, A549 and BEAS-2B cells, thermal stability at 37 °C, 32 °C and 4 °C, syncytia formation, neutralization by palivizumab and mucin mRNA expression in infected A549 cells. We observed that viruses isolated in one RSV season show differences on the tested assays. Furthermore, comparison with RSV A2 and RSV B1 reveals for some RSV isolates differences in viral replication kinetics, thermal stability and fusion capacity. Major differences are, however, not observed and differences between the recent isolates and reference strains is, overall, similar to the observed variation in between the recent isolates. One clinical isolate (BE/ANT-A11/17) replicated very efficiently in all cell lines, and remarkably, even better than RSV A2 in the HEp-2 cell line.
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15
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Sáez-López E, Cristóvão P, Costa I, Pechirra P, Conde P, Guiomar R, Peres MJ, Viseu R, Lopes P, Soares V, Vale F, Fonseca P, Freitas L, Alves J, Pessanha MA, Toscano C, Mota-Vieira L, Veloso RC, Côrte-Real R, Branquinho P, Pereira-Vaz J, Rodrigues F, Cunha M, Martins L, Mota P, Couto AR, Bruges-Armas J, Almeida S, Rodrigues D. Epidemiology and genetic variability of respiratory syncytial virus in Portugal, 2014-2018. J Clin Virol 2019; 121:104200. [PMID: 31707201 PMCID: PMC7106440 DOI: 10.1016/j.jcv.2019.104200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is associated with substantial morbidity and mortality since it is a predominant viral agent causing respiratory tract infections in infants, young children and the elderly. Considering the availability of the RSV vaccines in the coming years, molecular understanding in RSV is necessary. OBJECTIVE The objective of the present study was to describe RSV epidemiology and genotype variability in Portugal during the 2014/15-2017/18 period. MATERIAL AND METHODS Epidemiological data and RSV-positive samples from patients with a respiratory infection were collected through the non-sentinel and sentinel influenza surveillance system (ISS). RSV detection, subtyping in A and B, and sequencing of the second hypervariable region (HVR2) of G gene were performed by molecular methods. Phylogenetic trees were generated using the Neighbor-Joining method and p-distance model on MEGA 7.0. RESULTS RSV prevalence varied between the sentinel (2.5%, 97/3891) and the non-sentinel ISS (20.7%, 3138/16779), being higher (P < 0.0001) among children aged <5 years. Bronchiolitis (62.9%, 183/291) and influenza-like illness (24.6%, 14/57) were associated (P < 0.0001) with RSV laboratory confirmation among children aged <6 months and adults ≥65 years, respectively. The HVR2 was sequenced for 562 samples. RSV-A (46.4%, 261/562) and RSV-B (53.6%, 301/562) strains clustered mainly to ON1 (89.2%, 233/261) and BA9 (92%, 277/301) genotypes, respectively, although NA1 and BA10 were also present until 2015/2016. CONCLUSION The sequence and phylogenetic analysis reflected the relatively high diversity of Portuguese RSV strains. BA9 and ON1 genotypes, which have been circulating in Portugal since 2010/2011 and 2011/2012 respectively, predominated during the whole study period.
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Affiliation(s)
- Emma Sáez-López
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal; European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 16973, Solna, Sweden.
| | - Paula Cristóvão
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Inês Costa
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Pedro Pechirra
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Patrícia Conde
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Raquel Guiomar
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
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16
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Obando-Pacheco P, Justicia-Grande AJ, Rivero-Calle I, Rodríguez-Tenreiro C, Sly P, Ramilo O, Mejías A, Baraldi E, Papadopoulos NG, Nair H, Nunes MC, Kragten-Tabatabaie L, Heikkinen T, Greenough A, Stein RT, Manzoni P, Bont L, Martinón-Torres F. Respiratory Syncytial Virus Seasonality: A Global Overview. J Infect Dis 2019; 217:1356-1364. [PMID: 29390105 DOI: 10.1093/infdis/jiy056] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 01/24/2018] [Indexed: 11/12/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory infections in children. By the age of 1 year, 60%-70% of children have been infected by RSV. In addition, early-life RSV infection is associated with the development of recurrent wheezing and asthma in infancy and childhood. The need for precise epidemiologic data regarding RSV as a worldwide pathogen has been growing steadily as novel RSV therapeutics are reaching the final stages of development. To optimize the prevention, diagnosis, and treatment of RSV infection in a timely manner, knowledge about the differences in the timing of the RSV epidemics worldwide is needed. Previous analyses, based on literature reviews of individual reports obtained from medical databases, have failed to provide global country seasonality patterns. Until recently, only certain countries have been recording RSV incidence through their own surveillance systems. This analysis was based on national RSV surveillance reports and medical databases from 27 countries worldwide. This is the first study to use original-source, high-quality surveillance data to establish a global, robust, and homogeneous report on global country-specific RSV seasonality.
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Affiliation(s)
- Pablo Obando-Pacheco
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Galicia, Spain
| | - Antonio José Justicia-Grande
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Galicia, Spain
| | - Irene Rivero-Calle
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Galicia, Spain
| | - Carmen Rodríguez-Tenreiro
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Galicia, Spain
| | - Peter Sly
- Children's Lung Environment and Asthma Research, Child Health Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Octavio Ramilo
- Respiratory syncytial virus network (ReSViNET), Zeist.,Department of Pediatrics, Division of Infectious Diseases, Ohio State University, Columbus.,Center for Vaccines and Immunity at Nationwide Children's Hospital, Ohio State University, Columbus
| | - Asunción Mejías
- Respiratory syncytial virus network (ReSViNET), Zeist.,Department of Pediatrics, Division of Infectious Diseases, Ohio State University, Columbus.,Center for Vaccines and Immunity at Nationwide Children's Hospital, Ohio State University, Columbus
| | - Eugenio Baraldi
- Respiratory syncytial virus network (ReSViNET), Zeist.,Women's and Children's Health Department, University of Padova, Torino, Italy
| | - Nikolaos G Papadopoulos
- Respiratory syncytial virus network (ReSViNET), Zeist.,Department of Allergy, 2nd Pediatric Clinic, University of Athens, Greece.,Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Johannesburg, South Africa
| | - Harish Nair
- Respiratory syncytial virus network (ReSViNET), Zeist.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Johannesburg, South Africa
| | - Marta C Nunes
- Respiratory syncytial virus network (ReSViNET), Zeist.,Respiratory and Meningeal Pathogens Research Unit, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of Witwatersrand, Johannesburg, South Africa
| | - Leyla Kragten-Tabatabaie
- Respiratory syncytial virus network (ReSViNET), Zeist.,Julius Clinical, University Medical Center Utrecht, Zeist
| | - Terho Heikkinen
- Respiratory syncytial virus network (ReSViNET), Zeist.,Department of Pediatrics, University of Turku and Turku University Hospital, Finl
| | - Anne Greenough
- Respiratory syncytial virus network (ReSViNET), Zeist.,MRC & Asthma UK Centre for Allergic Mechanisms in Asthma, King's College London, Johannesburg, South Africa.,Department of Women and Children's Health, School of Life Course Sciences.,Faculty of Life Sciences and Medicine, King's College London
| | - Renato T Stein
- Respiratory syncytial virus network (ReSViNET), Zeist.,Pediatric Pulmonology Unit, Pontifícia Universidade Católica RS, Porto Alegre, Brazil
| | - Paolo Manzoni
- Respiratory syncytial virus network (ReSViNET), Zeist.,Neonataology and Neonatal Intensive Care Unit, S Anna Hospital, Torino, Italy
| | - Louis Bont
- Respiratory syncytial virus network (ReSViNET), Zeist.,Department of Pediatrics, University Medical Center Utrecht, The Netherlands.,Laboratory of Translational Immunology, University Medical Center Utrecht, The Netherlands
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Galicia, Spain.,Respiratory syncytial virus network (ReSViNET), Zeist
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17
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Liang X, Liu DH, Chen D, Guo L, Yang H, Shi YS, Wang YJ, Wang WK, Xie ZP, Gao HC, Duan ZJ, Zhang RF. Gradual replacement of all previously circulating respiratory syncytial virus A strain with the novel ON1 genotype in Lanzhou from 2010 to 2017. Medicine (Baltimore) 2019; 98:e15542. [PMID: 31083208 PMCID: PMC6531141 DOI: 10.1097/md.0000000000015542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
ON1 is a novel genotype of human respiratory syncytial virus (HRSV) subtype A, in children with acute respiratory tract infections (ARTIs). However, there is not much data on the prevalence and clinical and molecular characterization in China.Our study is based on the children who had respiratory infections positive for RSV-A admitted by Gansu Provincial Maternity and Child-care Hospital in Lanzhou (northwestern China) during the last 7 epidemic seasons from 2010 to 2017.In our study, different strains of the novel RSV-A genotype ON1, first identified in Canada in December 2010, were first detected in Gansu Provincial Maternity and Child-care Hospital in August 2012 and then followed by an abrupt expansion in the number of ON1 variants in the beginning of 2014 and eventually replaced all other RSV-A strains from 2015 to 2017. ON1 is characterized by a 72-nt duplication in the C-terminal region of the highly variable attachment glycoprotein (G), predicted to lengthen the polypeptide with 24 amino acids, including a 23-aa duplication, which likely changes antigenicity. New N-glycosylation sites occurred within the 23-aa duplication and 24-aa insertion of the ON1 viruses in our study. Notably, RSV infections occurred later, but peaked sooner from the 2014/2015 to 2016/2017 epidemic seasons, compared with the previous 4 seasons.Our study concluded that genotype ON1 has caused larger outbreaks and became the predominate genotype for HRSV subgroup A in Lanzhou from 2013 to 2017, and became the sole genotype of RSV-A in 2015/2016 and 2016/2017. Our data indicate that northwest of China and the world will eventually be dominated by the ON1 RSV-A genotype, including the possibility for vaccine development. Based on trends seen in RSV-B BA genotype, which predominated for decades, there is a possibility to develop a vaccine for children in the next 10 years.
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Affiliation(s)
- Xuan Liang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
- Gansu University of Chinese Medicine, Lanzhou
| | - Dong-Hai Liu
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
- Gansu University of Chinese Medicine, Lanzhou
| | - De Chen
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Li Guo
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Hui Yang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Yong-Sheng Shi
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Yong-Jun Wang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Wei-Kai Wang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou
| | - Zhi-Ping Xie
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Han-Chun Gao
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhao-Jun Duan
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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18
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Diagnostic accuracy of digital RNA quantification versus real-time PCR for the detection of respiratory syncytial virus in nasopharyngeal aspirates from children with acute respiratory infection. J Clin Virol 2018; 106:34-40. [PMID: 30031351 DOI: 10.1016/j.jcv.2018.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/12/2018] [Accepted: 07/13/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND Virus-specific molecular assays such as real-time polymerase chain reaction (RT-PCR) are regularly used as the gold standard to diagnose viral respiratory tract infections, but simultaneous detection of multiple different pathogens is often challenging. A multiplex digital method of RNA quantification, nCounter (NanoString Technologies), can overcome this disadvantage and identify, in a single reaction, the presence of different respiratory viruses. OBJECTIVES To evaluate the accuracy of nCounter to identify and quantify RSV-A and RSV-B in nasopharyngeal aspirates (NPA) of children (6-23-months-old) with acute respiratory infection. STUDY DESIGN NPA was collected at enrolment in a prospective cross-sectional study conducted in Salvador, Brazil. A quantitative RT-PCR with a subgroup-specific primer and probeset for RSV-A and RSV-B was performed in parallel with a customized nCounter probeset containing viral targets in NPA. RESULTS Of 559 NPA tested, RSV was detected by RT-PCR in 139 (24.9%), by nCounter in 122 (21.8%) and by any method in 158 (28.3%) cases. Compared to the gold standard of qRT-PCR, sensitivity of nCounter was 74.3% (95%CI:63.3%-82.9% RSV-A) and 77.6% (95%CI:66.3%-85.9% RSV-B); specificity was 98.4% (95%CI:96.8%-99.2% RSV-A) and 97.8% (95%CI:96.0%-98.8% RSV-B); positive predictive value was 87.3% (95%CI:76.9%-93.4% RSV-A) and 82.5% (95%CI:71.4%-90.0% RSV-B) and negative predictive value was 96.1% (95%CI:94.1%-97.5% RSV-A), and 96.9% (95%CI:95.1%-98.2% RSV-B). Accuracy was 95.2% (95%CI:93.1%-96.7%) for RSV-A and 95.3% (95%CI:93.3%-96.9%) for RSV-B, while both methods significantly correlated for RSV-A (r = 0.44, p = 8 × 10-5) and RSV-B (r = 0.73, p = 3 × 10-12) quantification. CONCLUSIONS nCounter is highly accurate in detecting RSV-A/B in NPA. Robustness and high-throughput multiplexing indicate its use in large-scale epidemiological studies.
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19
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Haider MSH, Khan WH, Deeba F, Ali S, Ahmed A, Naqvi IH, Dohare R, Alsenaidy HA, Alsenaidy AM, Broor S, Parveen S. BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics. PLoS One 2018; 13:e0193525. [PMID: 29694383 PMCID: PMC5919079 DOI: 10.1371/journal.pone.0193525] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 02/13/2018] [Indexed: 11/29/2022] Open
Abstract
Respiratory syncytial virus (RSV) is an important pathogen of global significance. The BA9 is one of the most predominant lineages of the BA genotype of group B RSV that has acquired a 60bp duplication in its G protein gene. We describe the local and global evolutionary dynamics of the second hyper variable region in the C- terminal of the G protein gene of the BA9 lineage. A total of 418 sequences (including 31 study and 387 GenBank strains) from 29 different countries were used for phylogenetic analysis. This analysis showed that the study strains clustered with BA (BA9 and BA8) and SAB4 genotype of group B RSV. We performed time-scaled evolutionary clock analyses using Bayesian Markov chain Monte Carlo methods. We also carried out glycosylation, selection pressure, mutational, entropy and Network analyses of the BA9 lineage. The time to the most recent common ancestor (tMRCA) of the BA genotype and BA9 lineage were estimated to be the years 1995 (95% HPD; 1987–1997) and 2000 (95% HPD; 1998–2001), respectively. The nucleotide substitution rate of the BA genotype [(4.58×10−3 (95% HPD; 3.89–5.29×10−3) substitution/site/year] was slightly faster than the BA9 lineage [4.03×10−3 (95% HPD; 4.65–5.2492×10−3)]. The BA9 lineage was categorized into 3 sub lineages (I, II and III) based on the Bayesian and Network analyses. The local transmission pattern suggested that BA9 is the predominant lineage of BA viruses that has been circulating in India since 2002 though showing fluctuations in its effective population size. The BA9 lineage established its global distribution with report from 23 different countries over the past 16 years. The present study augments our understanding of RSV infection, its epidemiological dynamics warranting steps towards its overall global surveillance.
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Affiliation(s)
| | - Wajihul Hasan Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Farah Deeba
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- Centre for Excellence in Biotechnology Research, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Irshad H. Naqvi
- Dr. M. A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | | | | | - Shobha Broor
- Department of Microbiology, Faculty of Medicine and Health Science, Shree Guru Gobind Singh Tricentenary University, Gurgaon, Haryana, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- * E-mail: ,
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20
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Haider MSH, Deeba F, Khan WH, Naqvi IH, Ali S, Ahmed A, Broor S, Alsenaidy HA, Alsenaidy AM, Dohare R, Parveen S. Global distribution of NA1 genotype of respiratory syncytial virus and its evolutionary dynamics assessed from the past 11 years. INFECTION GENETICS AND EVOLUTION 2018; 60:140-150. [PMID: 29427763 DOI: 10.1016/j.meegid.2018.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 01/29/2023]
Abstract
Respiratory syncytial virus (RSV) is a potent pathogen having global distribution. The main purpose of this study was to gain an insight into distribution pattern of the NA1 genotype of group A RSV across the globe together with its evolutionary dynamics. We focused on the second hypervariable region of the G protein gene and used the same for Phylogenetic, Bayesian and Network analyses. Eighteen percent of the samples collected from 500 symptomatic pediatric patients with acute respiratory tract infection (ARI) were found to be positive for RSV during 2011-15 from New Delhi, India. Of these, group B RSV was predominant and clustered into two different genotypes (BA and SAB4). Similarly, group A viruses clustered into two genotypes (NA1 and ON1). The data set from the group A viruses included 543 sequences from 23 different countries including 67 strains from India. The local evolutionary dynamics suggested consistent virus population of NA1 genotype in India during 2009 to 2014. The molecular clock analysis suggested that most recent common ancestor of group A and NA1 genotype have emerged in during the years 1953 and 2000, respectively. The global evolutionary rates of group A viruses and NA1 genotype were estimated to be 3.49 × 10-3 (95% HPD, 2.90-4.17 × 10-3) and 3.56 × 10-3 (95% HPD, 2.91 × 10-3-4.18 × 10-3) substitution/site/year, respectively. Analysis of the NA1 genotype of group A RSV reported during 11 years i.e. from 2004 to 2014 showed its dominance in 21 different countries across the globe reflecting its evolutionary dynamics. The Network analysis showed highly intricate but an inconsistent pattern of haplotypes of NA1 genotype circulating in the world. Present study seems to be first comprehensive attempt on global distribution and evolution of NA1 genotype augmenting the optimism towards the vaccine development.
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Affiliation(s)
| | - Farah Deeba
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Wajihul Hasan Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Irshad H Naqvi
- Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shobha Broor
- Department of Microbiology, Faculty of Medicine and Health Science, Shree Guru Gobind Singh Tricentenary University, Gurgaon, Haryana, India
| | | | | | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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21
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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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22
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Korsun N, Angelova S, Tzotcheva I, Georgieva I, Lazova S, Parina S, Alexiev I, Perenovska P. Prevalence and genetic characterisation of respiratory syncytial viruses circulating in Bulgaria during the 2014/15 and 2015/16 winter seasons. Pathog Glob Health 2017; 111:351-361. [PMID: 28948867 DOI: 10.1080/20477724.2017.1375708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The respiratory syncytial virus (RSV) is a leading cause of acute respiratory illnesses (ARI) in infants and young children. The objectives of this study were to investigate the RSV circulation among children aged <5 years in Bulgaria, to identify the RSV-A and RSV-B genotypes and to perform an amino acid sequence analysis of second hypervariable region (HVR2) of the G gene. During the 2014/15 and 2015/16 winter seasons, nasopharyngeal specimens of 610 children aged <5 years with ARI were tested using Real Time RT-PCR for influenza viruses, RSV, metapneumovirus, parainfluenza viruses, rhinoviruses and adenoviruses. Viral respiratory pathogens were detected in 429 (70%) out of 610 patients examined and RSV was the most frequently identified virus (26%) followed by influenza A(H1N1)pdm09 virus (14%) (p < .05). RSV was the most prevalent pathogen in patients with bronchiolitis (48%) and pneumonia (38%). In the 2014/15 season, RSV-A dominated slightly (53%), while in the next season RSV-B viruses prevailed more strongly (66%). The phylogenetic analysis based on the G gene indicated that all 21 studied RSV-A strains belonged to the ON1 genotype; the vast majority (96%) of the RSV-B strains were classified into BA9 genotype and only one - into BA10 genotype. All Bulgarian RSV-A and RSV-B sequences contained a 72-nt and a 60-nt duplication in the HVR2, respectively. The study showed the leading role of this pathogen as a causative agent of serious respiratory illnesses in early childhood, year-on-year fluctuations in RSV incidence, a shift from RSV-A to RSV-B subgroup dominance and relatively low genetic divergence in the circulating strains.
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Affiliation(s)
- Neli Korsun
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Svetla Angelova
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Iren Tzotcheva
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Irina Georgieva
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Snezhina Lazova
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Snezhana Parina
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Ivaylo Alexiev
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Penka Perenovska
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
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23
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Van der Gucht W, Leemans A, De Schryver M, Heykers A, Caljon G, Maes L, Cos P, Delputte PL. Respiratory syncytial virus (RSV) entry is inhibited by serine protease inhibitor AEBSF when present during an early stage of infection. Virol J 2017; 14:157. [PMID: 28818113 PMCID: PMC5561636 DOI: 10.1186/s12985-017-0824-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022] Open
Abstract
Background Host proteases have been shown to play important roles in many viral activities such as entry, uncoating, viral protein production and disease induction. Therefore, these cellular proteases are putative targets for the development of antivirals that inhibit their activity. Host proteases have been described to play essential roles in Ebola, HCV, HIV and influenza, such that specific protease inhibitors are able to reduce infection. RSV utilizes a host protease in its replication cycle but its potential as antiviral target is unknown. Therefore, we evaluated the effect of protease inhibitors on RSV infection. Methods To measure the sensitivity of RSV infection to protease inhibitors, cells were infected with RSV and incubated for 18 h in the presence or absence of the inhibitors. Cells were fixed, stained and studied using fluorescence microscopy. Results Several protease inhibitors, representing different classes of proteases (AEBSF, Pepstatin A, E-64, TPCK, PMSF and aprotinin), were tested for inhibitory effects on an RSV A2 infection of HEp-2 cells. Different treatment durations, ranging from 1 h prior to inoculation and continuing for 18 h during the assay, were evaluated. Of all the inhibitors tested, AEBSF and TPCK significantly decreased RSV infection. To ascertain that the observed effect of AEBSF was not a specific feature related to HEp-2 cells, A549 and BEAS-2B cells were also used. Similar to HEp-2, an almost complete block in the number of RSV infected cells after 18 h of incubation was observed and the effect was dose-dependent. To gain insight into the mechanism of this inhibition, AEBSF treatment was applied during different phases of an infection cycle (pre-, peri- and post-inoculation treatment). The results from these experiments indicate that AEBSF is mainly active during the early entry phase of RSV. The inhibitory effect was also observed with other RSV isolates A1998/3–2 and A2000/3–4, suggesting that this is a general feature of RSV. Conclusion RSV infection can be inhibited by broad serine protease inhibitors, AEBSF and TPCK. We confirmed that AEBSF inhibition is independent of the cell line used or RSV strain. The time point at which treatment with the inhibitor was most potent, was found to coincide with the expected moment of entry of the virion with the host cell.
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Affiliation(s)
- Winke Van der Gucht
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Annelies Leemans
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Marjorie De Schryver
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Annick Heykers
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Peter L Delputte
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium.
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Bouzas ML, Oliveira JR, Fukutani KF, Borges IC, Barral A, Van der Gucht W, Wollants E, Van Ranst M, de Oliveira CI, Van Weyenbergh J, Nascimento-Carvalho CM. Respiratory syncytial virus a and b display different temporal patterns in a 4-year prospective cross-sectional study among children with acute respiratory infection in a tropical city. Medicine (Baltimore) 2016; 95:e5142. [PMID: 27741144 PMCID: PMC5072971 DOI: 10.1097/md.0000000000005142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most common etiological agents of childhood respiratory infections globally. Information on seasonality of different antigenic groups is scarce. We aimed to describe the frequency, seasonality, and age of children infected by RSV antigenic groups A (RSVA) and B (RSVB) among children with ARI in a 4-year period.Children (6-23 months old) with respiratory infection for ≤7 days were enrolled in a prospective cross-sectional study, from September, 2009 to October, 2013, in Salvador, in a tropical region of Brazil. Upon recruitment, demographic, clinical data, and nasopharyngeal aspirates (NPA) were collected. A multiplex quantitative real-time polymerase chain reaction (RT-PCR) with a group-specific primer and probeset for RSVA and RSVB was used. Seasonal distribution of infection by RSV different antigenic groups was evaluated by Prais-Wisten regression.Of 560 cases, the mean age was 11.4 ± 4.5 months and there were 287 (51.3%) girls. Overall, RSV was detected in 139 (24.8%; 95% CI: 21.4%-28.5%) cases, RSVA in 74 (13.2%; 95% CI: 10.6%-16.2%) cases, and RSVB in 67 (12.0%; 95% CI: 9.5%-14.9%) cases. Two (0.4%; 95% CI: 0.06%-1.2%) cases had coinfection. RSVA frequency was 9.6%, 18.4%, 21.6%, and 3.1% in 2010, 2011, 2012, and 2013, respectively. RSVB frequency was 19.2%, 0.7%, 1.4%, and 35.4% in the same years. RSVA was more frequently found from August to January than February to July (18.2% vs. 6.4%, P < 0.001). RSVB was more frequently found (P < 0.001) between March and June (36.0%) than July to October (1.0%) or November to February (1.6%). RSVB infection showed seasonal distribution and positive association with humidity (P = 0.02) whereas RSVA did not. RSVA was more common among children ≥1-year-old (17.8% vs. 1.8%; P = 0.02), as opposed to RSVB (11.5% vs. 12.2%; P = 0.8).One quarter of patients had RSV infection. RSVA compromised more frequently children aged ≥1 year. RSVA predominated in 2011 and 2012 whereas RSVB predominated in 2010 and 2013. In regard to months, RSVA was more frequent from August to January whereas RSVB was more often detected between March and June. Markedly different monthly as well as yearly patterns for RSVA and RSVB reveal independent RSV antigenic groups' epidemics.
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Affiliation(s)
- Maiara L Bouzas
- Postgraduate Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Bahia, Brazil Centro de Pesquisas Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil Department of Pathology, Federal University of Bahia School of Medicine, Salvador, Bahia, Brazil Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU, Leuven, Belgium Department of Pediatrics, Federal University of Bahia School of Medicine, Salvador, Bahia, Brazil
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Structural, antigenic and immunogenic features of respiratory syncytial virus glycoproteins relevant for vaccine development. Vaccine 2016; 35:461-468. [PMID: 27692522 DOI: 10.1016/j.vaccine.2016.09.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/22/2016] [Indexed: 11/22/2022]
Abstract
Extraordinary progress in the structure and immunobiology of the human respiratory syncytial virus glycoproteins has been accomplished during the last few years. Determination of the fusion (F) glycoprotein structure folded in either the prefusion or the postfusion conformation was an inspiring breakthrough not only to understand the structural changes associated with the membrane fusion process but additionally to appreciate the antigenic intricacies of the F protein. Furthermore, these developments have opened new avenues for structure-based designs of promising hRSV vaccine candidates. Finally, recent advances in our knowledge of the attachment (G) glycoprotein and its interaction with cell-surface receptors have revitalized interest in this molecule as a vaccine, as well as its role in hRSV immunobiology.
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Zou L, Yi L, Wu J, Song Y, Huang G, Zhang X, Liang L, Ni H, Pybus OG, Ke C, Lu J. Evolution and Transmission of Respiratory Syncytial Group A (RSV-A) Viruses in Guangdong, China 2008-2015. Front Microbiol 2016; 7:1263. [PMID: 27574518 PMCID: PMC4983572 DOI: 10.3389/fmicb.2016.01263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/02/2016] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial viruses (RSVs) including subgroups A (RSV-A) and B (RSV-B) are an important cause of acute respiratory tract infections worldwide. RSV-A include major epidemic strains. Fundamental questions concerning the evolution, persistence and transmission of RSV-A are critical for disease control and prevention, yet remain unanswered. In this study, we generated 64 complete G gene sequences of RSV-A strains collected between 2008 and 2015 in Guangdong, China. Phylogenetic analysis was undertaken by incorporating 572 publicly available RSV-A sequences. Current data indicate that genotypes GA1, GA4, and GA5 are endemic with limited epidemic activity. In contrast, the GA2 genotype which likely originated in 1980 has spread rapidly and caused epidemics worldwide. By analyzing GA2 genotype sequences across epidemic seasons within Guangdong, we find that RSV-A epidemics in Guangdong are caused by a combination of virus importation and local persistence, although the magnitude of the latter is likely overestimated due to infrequent sampling in other regions. Our results provide new insights into RSV-A evolution and transmission at global and local scales and highlights the rapid and wide spread of genotype GA2 compared to other genotypes. In order to control RSV transmission and outbreak, both local persistence and external introduction should be taken into account when designing optimal strategies.
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Affiliation(s)
- Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Yingchao Song
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Guofeng Huang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Xin Zhang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Lijun Liang
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Hanzhong Ni
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | | | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention Guangzhou, China
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and PreventionGuangzhou, China; Department of Zoology, University of OxfordOxford, UK
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27
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Otieno JR, Agoti CN, Gitahi CW, Bett A, Ngama M, Medley GF, Cane PA, Nokes DJ. Molecular Evolutionary Dynamics of Respiratory Syncytial Virus Group A in Recurrent Epidemics in Coastal Kenya. J Virol 2016; 90:4990-5002. [PMID: 26937038 PMCID: PMC4859726 DOI: 10.1128/jvi.03105-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/25/2016] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED The characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing the efficiency of preexisting immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 to 2012) in Kilifi (n = 649), Kenya, and contemporaneous sequences (n = 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2 and then GA2 by ON1. Within these genotypes, there was considerable variation in potential N-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi data set was estimated at 3.58 × 10(-3) (95% highest posterior density interval = 3.04 to 4.16) nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating RSV-A strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics. IMPORTANCE The mechanisms underlying recurrent epidemics of RSV are poorly understood. We observe high genetic diversity in circulating strains within and between epidemics in both local and global settings. On longer time scales (∼7 years) there is sequential replacement of genotypes, whereas on shorter time scales (one epidemic to the next or within epidemics) there is a high turnover of variants within genotypes. Further, this genetic diversity is predicted to be associated with variation in antigenic profiles. These observations provide an explanation for recurrent RSV epidemics and have potential implications on the long-term effectiveness of vaccines.
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Affiliation(s)
- James R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biomedical Sciences, Pwani University, Kilifi, Kenya
| | - Caroline W Gitahi
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ann Bett
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Mwanajuma Ngama
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Graham F Medley
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and WIDER, University of Warwick, Coventry, United Kingdom
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Trento A, Ábrego L, Rodriguez-Fernandez R, González-Sánchez MI, González-Martínez F, Delfraro A, Pascale JM, Arbiza J, Melero JA. Conservation of G-Protein Epitopes in Respiratory Syncytial Virus (Group A) Despite Broad Genetic Diversity: Is Antibody Selection Involved in Virus Evolution? J Virol 2015; 89:7776-85. [PMID: 25995258 PMCID: PMC4505632 DOI: 10.1128/jvi.00467-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/11/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Worldwide G-glycoprotein phylogeny of human respiratory syncytial virus (hRSV) group A sequences revealed diversification in major clades and genotypes over more than 50 years of recorded history. Multiple genotypes cocirculated during prolonged periods of time, but recent dominance of the GA2 genotype was noticed in several studies, and it is highlighted here with sequences from viruses circulating recently in Spain and Panama. Reactivity of group A viruses with monoclonal antibodies (MAbs) that recognize strain-variable epitopes of the G glycoprotein failed to correlate genotype diversification with antibody reactivity. Additionally, no clear correlation was found between changes in strain-variable epitopes and predicted sites of positive selection, despite both traits being associated with the C-terminal third of the G glycoprotein. Hence, our data do not lend support to the proposed antibody-driven selection of variants as a major determinant of hRSV evolution. Other alternative mechanisms are considered to account for the high degree of hRSV G-protein variability. IMPORTANCE An unusual characteristic of the G glycoprotein of human respiratory syncytial virus (hRSV) is the accumulation of nonsynonymous (N) changes at higher rates than synonymous (S) changes, reaching dN/dS values at certain sites predictive of positive selection. Since these sites cluster preferentially in the C-terminal third of the G protein, like certain epitopes recognized by murine antibodies, it was proposed that immune (antibody) selection might be driving the apparent positive selection, analogous to the antigenic drift observed in the influenza virus hemagglutinin (HA). However, careful antigenic and genetic comparison of the G glycoprotein does not provide evidence of antigenic drift in the G molecule, in agreement with recently published data which did not indicate antigenic drift in the G protein with human sera. Alternative explanations to the immune-driven selection hypothesis are offered to account for the high level of G-protein genetic diversity highlighted in this study.
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Affiliation(s)
- Alfonsina Trento
- Unidad de Biología Viral, Centro Nacional de Microbiología, Madrid, Spain CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Leyda Ábrego
- Departamento de Investigación en Virología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panamá, Panama
| | | | | | | | - Adriana Delfraro
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Juan M Pascale
- Departamento de Investigación en Virología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panamá, Panama
| | - Juan Arbiza
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - José A Melero
- Unidad de Biología Viral, Centro Nacional de Microbiología, Madrid, Spain CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Salimi V, Tavakoli-Yaraki M, Yavarian J, Bont L, Mokhtari-Azad T. Prevalence of human respiratory syncytial virus circulating in Iran. J Infect Public Health 2015; 9:125-35. [PMID: 26143136 DOI: 10.1016/j.jiph.2015.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/14/2015] [Accepted: 05/02/2015] [Indexed: 01/14/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infection during early childhood and is associated with a great burden on patients, parents, and society. While no treatment is yet available, results from recent phase 2 clinical trials of cell-entry inhibitors and RSV vaccines are promising. To prepare for introduction of these novel therapeutics, good understanding of its molecular epidemiology and continuous RSV surveillance data are necessary. This paper provides an overview of RSV prevalence and genotype distribution in Iran from 1996 to 2013. This meta-analysis includes 21 published studies. In total, 775 (18.7%) of 4140 respiratory specimens were positive for RSV infection. The male-female ratio of RSV-positive patients was 1.5:1. Significant peaks of RSV infection were detected during the cold season (November-March). RSV infection was mainly observed in patients <2 years of age. Phylogenetic studies showed that genotypes GA1, GA2, GA5, and BA co-circulated in Iran in 2007-2013. This review highlights the necessity of introducing standard molecular surveillance programs to inform the epidemiological, clinical, and pathological characteristics of various RSV genotypes. Improved understanding of the molecular epidemiology will be useful for development of novel RSV therapeutics.
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Affiliation(s)
- Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Masoumeh Tavakoli-Yaraki
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Jila Yavarian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Louis Bont
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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30
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Fukutani KF, Nascimento-Carvalho CM, Van der Gucht W, Wollants E, Khouri R, Dierckx T, Van Ranst M, Houspie L, Bouzas ML, Oliveira JR, Barral A, Van Weyenbergh J, de Oliveira CI. Pathogen transcriptional profile in nasopharyngeal aspirates of children with acute respiratory tract infection. J Clin Virol 2015. [PMID: 26209405 PMCID: PMC7106536 DOI: 10.1016/j.jcv.2015.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
nCounter enables detection of pathogen transcripts in NPA with low RNA input. nCounter detects, in a single reaction, the presence of multiple pathogens in NPA. nCounter displayed a good agreement with Real-Time PCR for RSV.
Background Acute respiratory tract infections (ARI) present a significant morbidity and pose a global health burden. Patients are frequently treated with antibiotics although ARI are most commonly caused by virus, strengthening the need for improved diagnostic methods. Objectives Detect viral and bacterial RNA in nasopharyngeal aspirates (NPA) from children aged 6–23 months with ARI using nCounter. Study design A custom-designed nCounter probeset containing viral and bacterial targets was tested in NPA of ARI patients. Results Initially, spiked control viral RNAs were detectable in ≥6.25 ng input RNA, indicating absence of inhibitors in NPA. nCounter applied to a larger NPA sample (n = 61) enabled the multiplex detection of different pathogens: RNA viruses Parainfluenza virus (PIV 1–3) and RSV A-B in 21%, Human metapneumovirus (hMPV) in 5%, Bocavirus (BoV), CoV, Influenza virus (IV) A in 3% and, Rhinovirus (RV) in 2% of samples, respectively. RSV A-B was confirmed by Real Time PCR (86.2–96.9% agreement). DNA virus (AV) was detected at RNA level, reflecting viral replication, in 10% of samples. Bacterial transcripts from Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae and Chlamydophila pneumoniae were detected in 77, 69, 26, 8, 3 and 2% of samples, respectively. Conclusion nCounter is robust and sensitive for the simultaneous detection of viral (both RNA and DNA) and bacterial transcripts in NPA with low RNA input (<10 ng). This medium-throughput technique will increase our understanding of ARI pathogenesis and may provide an evidence-based approach for the targeted and rational use of antibiotics in pediatric ARI.
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Affiliation(s)
- Kiyoshi F Fukutani
- Centro de Pesquisas Gonçalo Moniz (CPqGM)-FIOCRUZ, Salvador, BA, Brazil; Post-Graduation Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Brazil
| | - Cristiana M Nascimento-Carvalho
- Post-Graduation Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Brazil; Department of Pediatrics, School of Medicine, Federal University of Bahia, Salvador, BA, Brazil
| | - Winke Van der Gucht
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Elke Wollants
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ricardo Khouri
- Centro de Pesquisas Gonçalo Moniz (CPqGM)-FIOCRUZ, Salvador, BA, Brazil; Post-Graduation Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Brazil
| | - Tim Dierckx
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Lieselot Houspie
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Maiara L Bouzas
- Post-Graduation Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Brazil
| | - Juliana R Oliveira
- Post-Graduation Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Brazil
| | - Aldina Barral
- Centro de Pesquisas Gonçalo Moniz (CPqGM)-FIOCRUZ, Salvador, BA, Brazil; Post-Graduation Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Brazil; Department of Pathology, School of Medicine, Federal University of Bahia, Salvador, BA, Brazil; Instituto de Investigação em Imunologia, São Paulo, SP, Brazil
| | - Johan Van Weyenbergh
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Camila I de Oliveira
- Centro de Pesquisas Gonçalo Moniz (CPqGM)-FIOCRUZ, Salvador, BA, Brazil; Post-Graduation Program in Health Sciences, Federal University of Bahia School of Medicine, Salvador, Brazil; Instituto de Investigação em Imunologia, São Paulo, SP, Brazil.
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Yu X, Kou Y, Xia D, Li J, Yang X, Zhou Y, He X. Human respiratory syncytial virus in children with lower respiratory tract infections or influenza-like illness and its co-infection characteristics with viruses and atypical bacteria in Hangzhou, China. J Clin Virol 2015. [PMID: 26209367 PMCID: PMC7185398 DOI: 10.1016/j.jcv.2015.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is the most important viral pathogen in children. However, its epidemic patterns and co-infection characteristics are not fully understood. OBJECTIVES We attempted to determine the level of genetic variation of RSV, and describe the prevalence and co-infection characteristics of RSV in Hangzhou during two epidemic seasons. STUDY DESIGN Single respiratory samples from 1820 pediatric patients were screened for RSV and genotyped by RT-PCR and sequencing. In all RSV positive specimens, we screened for viruses and atypical bacteria. Demographic and clinical information was recorded and analyzed. RESULTS A total of 34.5% and 3.8% of samples from acute lower respiratory tract infections (ALRI) and influenza-like illness (ILI) were positive for RSV, respectively. Phylogenetic analysis revealed that 61.1% of the selected 167 RSV strains were NA1, 31.1% were BA, 3.6% were ON1, 2.4% were CB1, and 1.8% were NA3. A new genotype, BA11 was identified, which comprised 98.1% of BA strains in this study, while the rest were BA10. A total of 36.4% and 9.1% of RSV-positive children with ALRI and ILI respectively were found to be co-infected. Rhinovirus was the most common additional respiratory virus, followed by human metapneumovirus. Except for fever, no significant differences in other clinical presentation between the RSV mono-infection and co-infection groups were observed. CONCLUSIONS The circulating RSV strains had high genetic variability with RSV-B showing a more local pattern. In ALRI cases, co-infection of RSV with other viruses or atypical bacteria has no significant effect on the clinical presentation except fever.
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Affiliation(s)
- Xinfen Yu
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China.
| | - Yu Kou
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Daozong Xia
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jun Li
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Xuhui Yang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Yinyan Zhou
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaoyan He
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
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Pierangeli A, Trotta D, Scagnolari C, Ferreri ML, Nicolai A, Midulla F, Marinelli K, Antonelli G, Bagnarelli P. Rapid spread of the novel respiratory syncytial virus A ON1 genotype, central Italy, 2011 to 2013. Euro Surveill 2014; 19. [DOI: 10.2807/1560-7917.es2014.19.26.20843] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Respiratory infections positive for human respiratory syncytial virus (RSV) subtype A were characterised in children admitted to hospitals in Rome and Ancona (Italy) over the last three epidemic seasons. Different strains of the novel RSV-A genotype ON1, first identified in Ontario (Canada) in December 2010, were detected for the first time in Italy in the following 2011/12 epidemic season. They bear an insertion of 24 amino acids in the G glycoprotein as well as amino acid changes likely to change antigenicity. By early 2013, ON1 strains had spread so efficiently that they had nearly replaced other RSV-A strains. Notably, the RSV peak in the 2012/13 epidemic season occurred earlier and, compared with the previous two seasons, influenza-like illnesses diagnoses were more frequent in younger children; bronchiolitis cases had a less severe clinical course. Nonetheless, the ON1-associated intensive care unit admission rate was similar, if not greater, than that attributable to other RSV-A strains. Improving RSV surveillance would allow timely understanding of the epidemiological and clinicopathological features of the novel RSV-A genotype.
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Affiliation(s)
- A Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - D Trotta
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
| | - C Scagnolari
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - M L Ferreri
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
| | - A Nicolai
- Department of Paediatrics, Sapienza University, Rome, Italy
| | - F Midulla
- Department of Paediatrics, Sapienza University, Rome, Italy
| | - K Marinelli
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
| | - G Antonelli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - P Bagnarelli
- Department of Biomedical Sciences and Public Health, Virology Unit, Università Politecnica Marche, Ancona, Italy
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Faghihloo E, Yavarian J, Jandaghi NZS, Shadab A, Azad TM. Genotype circulation pattern of human respiratory syncytial virus in Iran. INFECTION GENETICS AND EVOLUTION 2014; 22:130-3. [PMID: 24462624 DOI: 10.1016/j.meegid.2014.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/22/2013] [Accepted: 01/13/2014] [Indexed: 11/29/2022]
Abstract
In order to have information on the molecular epidemiology and genetic circulation pattern of human respiratory syncytial virus (HRSV) in Iran, we studied the genetic variability of both group A and B HRSV strains during seven consecutive years by sequencing the hypervariable C-terminal domain of G protein. A total of 485 children <2years of age who were negative for influenza viruses, screened for the presence of HRSV in this research. HRSV was detected in 94 (19.38%) of the samples using nested RT-PCR. Group A viruses were isolated during each year, while group B viruses were isolated during 2009 and 2013. Phylogenetic analysis showed that all HRSV group A viruses belonged to three genotypes: GA1, GA2, GA5 and the group B viruses were in BA genotype.
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Affiliation(s)
- Ebrahim Faghihloo
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
| | - Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
| | | | - Azadeh Shadab
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
| | - Talat Mokhtari Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
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