51
|
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.
Collapse
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
| |
Collapse
|
52
|
Zheng Y, Liu L, Wang S, Li Z, Hou M, Li J, Yu XF, Zhang W, Hua S. Prevailing genotype distribution and characteristics of human respiratory syncytial virus in northeastern China. J Med Virol 2016; 89:222-233. [PMID: 27448044 PMCID: PMC5157725 DOI: 10.1002/jmv.24640] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2016] [Indexed: 01/10/2023]
Abstract
Although human respiratory syncytial virus (RSV) is one of the most common viruses inducing respiratory tract infections in young children and the elderly, the genotype distribution and characteristics of RSV in northeastern China have not been investigated. Here, we identified 25 RSV‐A and 8 RSV‐B strains from 80 samples of patients with respiratory infections between February 2015 and May 2015. All 25 RSV‐A viruses were classified as the ON1 genotype, which rapidly spread and became the dominant genotype in the world since being identified in Ontario (Canada) in December 2010. All eight RSV‐B viruses belonged to the BA genotype with a 60‐nucleotide duplication, seven of which formed two new genotypes, BA‐CCA and BA‐CCB. The remaining RSV‐B virus clustered with one of the Hangzhou strains belonging to genotype BA11. Construction of a phylogenetic tree and amino acid substitution analysis showed that Changchun ON1 viruses exclusively constituted Lineages 3, 5 and 6, and contained several unique and newly identified amino acid substitutions, including E224G, R244K, L289I, Y297H, and L298P. Selective pressure was also evaluated, and various N and O‐glycosylation sites were predicted. This study provides the first genetic analysis of RSV in northeastern China and may facilitate a better understanding of the evolution of this virus locally and globally. J. Med. Virol. 89:222–233, 2017. © 2016 The Authors. Journal of Medical Virology Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Yuxuan Zheng
- Department of Respiratory Medicine, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Li Liu
- Department of Pediatric Respiratory Medicine, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Shaohua Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Zhaolong Li
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Min Hou
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Jingliang Li
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Xiao-Fang Yu
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Shucheng Hua
- Department of Respiratory Medicine, First Hospital of Jilin University, Changchun, Jilin Province, China
| |
Collapse
|
53
|
Fan R, Fan C, Zhang J, Wen B, Lei Y, Liu C, Chen L, Liu W, Wang C, Qu X. Respiratory syncytial virus subtype ON1/NA1/BA9 predominates in hospitalized children with lower respiratory tract infections. J Med Virol 2016; 89:213-221. [PMID: 27358012 PMCID: PMC7166484 DOI: 10.1002/jmv.24619] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 12/02/2022]
Abstract
Respiratory syncytial virus (RSV) infection is the leading cause of acute respiratory tract disease in children less than 5 years old. The aim of this study was to further elucidate the molecular properties and clinical characteristics of RSV infection. The study sample included 238 patients <5 years old who were hospitalized with clinical symptoms of upper or lower respiratory tract infection (URTI or LRTI) in the Pediatric Department at the First People's Hospital of Chenzhou, South China in 2014. We subjected nasopharyngeal aspirate (NPA) or nasal swab (NS) samples from the patients to indirect fluorescence assay screens. RSV G genes were amplified by reverse transcription‐PCR (RT‐PCR) and sequenced. Of the 238 patients screened, 64 (26.8%) were confirmed to have RSV infections. Of those 64 confirmed RSV infection cases, 39 (60.9%) had subtype BA9, 13 (20.3%) had the recently identified subtype ON1, 11 (17.2%) had subtype NA1, and 1 (1.6%) had subtype GB2. The predominant presentation was LRTI with coughing, sputum production, fever, and wheezing. RSV subtype NA1 and BA9 infections were found mostly in infants, whereas the age distribution of subtype ON1 infections was more uniform across the age bands. Phylogenetic analysis indicated that, compared with the prototype strain A2, all ON1 and most NA1 isolates had lost one potential N‐glycosylation site at amino acid 251 and 249 due to T251K and N249Y substitution, respectively. These findings suggest that NA1, BA9, and ON1 are the dominant RSV subtypes causing respiratory tract infections in young children presenting to the hospital in South China. J. Med. Virol. 89:213–221, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ruyan Fan
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China.,Department of Pediatric, Guangzhou Women and Children's Medical Center, Guangzhou, People's Republic of China
| | - Chuping Fan
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Jian Zhang
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Bo Wen
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Yefei Lei
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Chan Liu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Lijuan Chen
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Wenpei Liu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| | - Chuan Wang
- Department of Public Health, Sichuan University, Chengdu, People's Republic of China
| | - Xiaowang Qu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Throughput Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, University of South China, Chenzhou, People's Republic of China
| |
Collapse
|
54
|
Kadji FMN, Okamoto M, Furuse Y, Tamaki R, Suzuki A, Lirio I, Dapat C, Malasao R, Saito M, Pedrera-Rico GAG, Tallo V, Lupisan S, Saito M, Oshitani H. Differences in viral load among human respiratory syncytial virus genotypes in hospitalized children with severe acute respiratory infections in the Philippines. Virol J 2016; 13:113. [PMID: 27350282 PMCID: PMC4924256 DOI: 10.1186/s12985-016-0565-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 06/17/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Human respiratory syncytial virus (HRSV) is a leading viral etiologic agent of pediatric lower respiratory infections, including bronchiolitis and pneumonia. Two antigenic subgroups, HRSV-A and B, each contain several genotypes. While viral load may vary among HRSV genotypes and affect the clinical course of disease, data are scarce regarding the actual differences among genotypes. Therefore, this study estimated and compared viral load among NA1 and ON1 genotypes of HRSV-A and BA9 of HRSV-B. ON1 is a newly emerged genotype with a 72-nucleotide duplication in the G gene as observed previously with BA genotypes in HRSV-B. FINDINGS Children <5 years of age with an initial diagnosis of severe or very severe pneumonia at a hospital in the Philippines from September 2012 to December 2013 were enrolled. HRSV genotypes were determined and the viral load measured from nasopharyngeal swabs (NPS). The viral load of HRSV genotype NA1 were significantly higher than those of ON1 and BA9. Regression analysis showed that both genotype NA1 and younger age were significantly associated with high HRSV viral load. CONCLUSIONS The viral load of NA1 was higher than that of ON1 and BA9 in NPS samples. HRSV genotypes may be associated with HRSV viral load. The reasons and clinical impacts of these differences in viral load among HRSV genotypes require further evaluation.
Collapse
Affiliation(s)
| | - Michiko Okamoto
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuki Furuse
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Raita Tamaki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Suzuki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Irene Lirio
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, the Philippines
| | - Clyde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Mariko Saito
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, the Philippines
| | | | - Veronica Tallo
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Mayuko Saito
- Tohoku University Graduate School of Medicine, Sendai, Japan.
| | | |
Collapse
|
55
|
Association of RSV-A ON1 genotype with Increased Pediatric Acute Lower Respiratory Tract Infection in Vietnam. Sci Rep 2016; 6:27856. [PMID: 27306333 PMCID: PMC4910061 DOI: 10.1038/srep27856] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/26/2016] [Indexed: 12/26/2022] Open
Abstract
Since the initial discovery of RSV-A ON1 in Canada in 2010, ON1 has been reported worldwide, yet information regarding its clinical impact and severity has been controversial. To investigate the clinical relevance of RSV-A ON1,acute respiratory infection (ARI) cases enrolled to our population-based prospective pediatric ARI surveillance at Khanh Hoa General Hospital, Central Vietnam from January 2010 through December 2012 were studied. Clinical-epidemiological information and nasopharyngeal samples were collected. Multiplex PCR assays were performed for screening 13 respiratory viruses. RSV-positive samples were further tested for subgroups (A/B) and genotypes information by sequencing the G-glycoprotein 2nd hypervariable region. Statistical analysis was performed to evaluate the clinical-epidemiological characteristics of RSV-A ON1. A total of 1854 ARI cases were enrolled and 426 (23.0%) of them were RSV-positive. During the study period, RSV-A and B had been co-circulating. NA1 was the predominant RSV-A genotype until the appearance of ON1 in 2012. RSV-related ARI hospitalization incidence significantly increased after the emergence of ON1. Moreover, multivariate analysis revealed that risk of lower respiratory tract infection was 2.26 (95% CI: 1.37-3.72) times, and radiologically-confirmed pneumonia was 1.98 (95% CI: 1.01-3.87) times greater in ON1 compared to NA1 cases. Our result suggested that ON1 ARI cases were clinically more severe than NA1.
Collapse
|
56
|
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.
Collapse
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
| |
Collapse
|
57
|
Viegas M, Goya S, Mistchenko AS. Sixteen years of evolution of human respiratory syncytial virus subgroup A in Buenos Aires, Argentina: GA2 the prevalent genotype through the years. INFECTION GENETICS AND EVOLUTION 2016; 43:213-21. [PMID: 27154330 DOI: 10.1016/j.meegid.2016.04.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/28/2016] [Accepted: 04/30/2016] [Indexed: 01/06/2023]
Abstract
Human respiratory syncytial virus (HRSV) is the main viral cause of acute lower respiratory tract infections (LRTI) in children worldwide. In recent years, several preclinical trials with vaccine candidates have been reported. It is in this sense that molecular epidemiological studies become important. Understanding viral dispersion patterns before and after the implementation of a vaccine can provide insight into the effectiveness of the control strategies. In this work we analyzed the molecular epidemiology of HRSV-A over a period of sixteen years (1999-2014) in Buenos Aires. By bioinformatic tools we analyzed 169 sequences of the G glycoprotein gene from hospitalized pediatric patients with LRTI. We found that GA2 was the most prevalent genotype (73.35%). GA5 genotype co-circulated in our region until 2009 when it was no longer detected, except in 2011. The recently globally emerging ON1 lineage with a 72-nt duplication increased its frequency to become the only lineage detected in Buenos Aires in 2014. By discrete phylogeographic analysis of global ON1 strains we could determine that Panama could be the location of the MRCA dated June 20, 2010; and this lineage could be introduced in Argentina from Spain in April 2011. This analysis also showed temporary and geographical clustering of ON1 strains observed as phylogenetic clades with strains exclusively associated from a single country, nevertheless among our 44 ON1 strains from three outbreaks (2012-2014) we could also detect posterior reintroductions and circulation from United States, Cuba, South Korea, and Spain. The continuous phylogeographic analysis of one sublineage of Argentine ON1 strains allowed us to establish that there could be a local clustering of some strains even in neighborhoods. This work shows the potential of this type of bioinformatic tools in the context of a future vaccine surveillance network to trace the spread of new genetic lineages in human populations.
Collapse
Affiliation(s)
- M Viegas
- Virology Laboratory, Ricardo Gutiérrez Children's Hospital, Gallo 1330 2°, 1425 Ciudad Autónoma Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - S Goya
- Virology Laboratory, Ricardo Gutiérrez Children's Hospital, Gallo 1330 2°, 1425 Ciudad Autónoma Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - A S Mistchenko
- Virology Laboratory, Ricardo Gutiérrez Children's Hospital, Gallo 1330 2°, 1425 Ciudad Autónoma Buenos Aires, Argentina; Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC), Argentina.
| |
Collapse
|
58
|
Malasao R, Okamoto M, Chaimongkol N, Imamura T, Tohma K, Dapat I, Dapat C, Suzuki A, Saito M, Saito M, Tamaki R, Pedrera-Rico GAG, Aniceto R, Quicho RFN, Segubre-Mercado E, Lupisan S, Oshitani H. Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012-2013. PLoS One 2015; 10:e0142192. [PMID: 26540236 PMCID: PMC4635013 DOI: 10.1371/journal.pone.0142192] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/19/2015] [Indexed: 12/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of acute lower respiratory tract infections in infants and children worldwide. We performed molecular analysis of HRSV among infants and children with clinical diagnosis of severe pneumonia in four study sites in the Philippines, including Biliran, Leyte, Palawan, and Metro Manila from June 2012 to July 2013. Nasopharyngeal swabs were collected and screened for HRSV using real-time polymerase chain reaction (PCR). Positive samples were tested by conventional PCR and sequenced for the second hypervariable region (2nd HVR) of the G gene. Among a total of 1,505 samples, 423 samples were positive for HRSV (28.1%), of which 305 (72.1%) and 118 (27.9%) were identified as HRSV-A and HRSV-B, respectively. Two genotypes of HRSV-A, NA1 and ON1, were identified during the study period. The novel ON1 genotype with a 72-nucleotide duplication in 2nd HVR of the G gene increased rapidly and finally became the predominant genotype in 2013 with an evolutionary rate higher than the NA1 genotype. Moreover, in the ON1 genotype, we found positive selection at amino acid position 274 (p<0.05) and massive O- and N-glycosylation in the 2nd HVR of the G gene. Among HRSV-B, BA9 was the predominant genotype circulating in the Philippines. However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains. These findings suggest that HRSV is an important cause of severe acute respiratory infection among children in the Philippines and revealed the emergence and subsequent predominance of the ON1 genotype and the sporadic detection of the GB2 genotype. Both genotypes were detected for the first time in the Philippines.
Collapse
Affiliation(s)
| | - Michiko Okamoto
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | | | - Kentaro Tohma
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Isolde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Clyde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Suzuki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayuko Saito
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | - Raita Tamaki
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | | | - Rapunzel Aniceto
- Eastern Visayas Regional Medical Center, Tacloban City, Philippines
| | | | | | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | | |
Collapse
|
59
|
Duvvuri VR, Granados A, Rosenfeld P, Bahl J, Eshaghi A, Gubbay JB. Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: global and local transmission dynamics. Sci Rep 2015; 5:14268. [PMID: 26420660 PMCID: PMC4588507 DOI: 10.1038/srep14268] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/21/2015] [Indexed: 12/04/2022] Open
Abstract
Human respiratory syncytial virus (RSV) A ON1 genotype, first detected in 2010 in Ontario, Canada, has been documented in 21 countries to date. This study investigated persistence and transmission dynamics of ON1 by grouping 406 randomly selected RSV-positive specimens submitted to Public Health Ontario from August 2011 to August 2012; RSV-A-positive specimens were genotyped. We identified 370 RSV-A (181 NA1, 135 NA2, 51 ON1 3 GA5) and 36 RSV-B positive specimens. We aligned time-stamped second hypervariable region (330 bp) of G-gene sequence data (global, n = 483; and Ontario, n = 60) to evaluate transmission dynamics. Global data suggests that the most recent common ancestor of ON1 emerged during the 2008–2009 season. Mean evolutionary rate of the global ON1 was 4.10 × 10−3 substitutions/site/year (95% BCI 3.1–5.0 × 10−3), not significantly different to that of Ontario ON1. The estimated mean reproductive number (R0 = ∼ 1.01) from global and Ontario sequences showed no significant difference and implies stability among global RSV-A ON1. This study suggests that local epidemics exhibit similar underlying evolutionary and epidemiological dynamics to that of the persistent global RSV-A ON1 population. These findings underscore the importance of continual molecular surveillance of RSV in order to gain a better understanding of epidemics.
Collapse
Affiliation(s)
- Venkata R Duvvuri
- Public Health Ontario, Toronto, Ontario, Canada.,University of Waterloo, Waterloo, Ontario, Canada (MPH student)
| | - Andrea Granados
- Public Health Ontario, Toronto, Ontario, Canada.,University of Toronto, Ontario, Canada
| | | | - Justin Bahl
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, Texas, United States of America
| | | | - Jonathan B Gubbay
- Public Health Ontario, Toronto, Ontario, Canada.,University of Toronto, Ontario, Canada.,Mount Sinai Hospital, Toronto, Ontario, Canada.,The Hospital for Sick Children, Toronto, Ontario, Canada
| |
Collapse
|
60
|
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.
Collapse
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
| |
Collapse
|
61
|
Ivancic-Jelecki J, Forcic D, Mlinaric-Galinovic G, Tesovic G, Nikic Hecer A. Early Evolution of Human Respiratory Syncytial Virus ON1 Strains: Analysis of the Diversity in the C-Terminal Hypervariable Region of Glycoprotein Gene within the First 3.5 Years since Their Detection. Intervirology 2015; 58:172-80. [PMID: 26112390 DOI: 10.1159/000382018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/31/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Characterization of the phylogeny and diversity of human respiratory syncytial virus (HRSV) genotype ON1 that occurred during its early evolution (within the first 3.5 years since the detection of the first ON1 strains). ON1 strains have a 72-nucleotide-long in-frame duplication within the second hypervariable domain of the glycoprotein gene (HVR2). METHODS All available HVR2 sequences of strains belonging to the ON1 genotype published prior to June 20, 2014 were collected. Multiple sequence alignments, phylogeny, phylogeography, sequence clustering and putative protein analyses were performed. RESULTS The worldwide spread and diversification of ON1 strains are presented. Only in a minority of ON1 strains do the two replicas remain identical, and various ON1 strains possess common differences between the first and the second copy (segments A and B). Mutations of the progenitor sequence were more frequent in segment B, a higher overall diversity on the protein level and more putative glycosylation sites exist in segment B, and, unlike in segment A, positive selection acts on that protein region. CONCLUSIONS The fast spread of the novel HRSV genotype ON1 has been accompanied by its rapid concurrent diversification. Differences in variability of the two replicas within HVR2 were detected, with C-terminal replica being more variable.
Collapse
Affiliation(s)
- Jelena Ivancic-Jelecki
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia
| | | | | | | | | |
Collapse
|
62
|
Esposito S, Piralla A, Zampiero A, Bianchini S, Di Pietro G, Scala A, Pinzani R, Fossali E, Baldanti F, Principi N. Characteristics and Their Clinical Relevance of Respiratory Syncytial Virus Types and Genotypes Circulating in Northern Italy in Five Consecutive Winter Seasons. PLoS One 2015; 10:e0129369. [PMID: 26047100 PMCID: PMC4457818 DOI: 10.1371/journal.pone.0129369] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/07/2015] [Indexed: 12/30/2022] Open
Abstract
In order to investigate the genetic diversity and patterns of the co-circulating genotypes of respiratory syncytial virus (RSV) and their possible relationships with the severity of RSV infection, we studied all of the RSV-positive nasopharyngeal samples collected from children during five consecutive winters (2009–2010, 2010–2011, 2011–2012, 2012–2013 and 2013–2014). The RSVs were detected using the respiratory virus panel fast assay and single-tube RT-PCR, their nucleotides were sequenced, and they were tested for positive selection. Of the 165 positive samples, 131 (79.4%) carried RSV-A and 34 (20.6%) RSV-B; both groups co-circulated in all of the study periods, with RSV-A predominating in all the seasons except for winter 2010–2011, which had a predominance of RSV-B. Phylogenetic analysis of the RSV-A sequences identified genotypes NA1 and ON1, the second replacing the first during the last two years of the study period. The RSV-B belonged to genotypes BA9 and BA10. BA9 was detected in all the years of the study whereas BA only desultorily. Comparison of the subjects infected by RSV-A and RSV-B types did not reveal any significant differences, but the children infected by genotype A/NA1 more frequently had lower respiratory tract infections (p<0.0001) and required hospitalisation (p = 0.007) more often than those infected by genotype A/ON1. These findings show that RSV has complex patterns of circulation characterised by the periodical replacement of the predominant genotypes, and indicate that the circulation and pathogenic role of the different RSV strains should be investigated as each may have a different impact on the host. A knowledge of the correlations between types, genotypes and disease severity may also be important in order to be able to include the more virulent strains in future vaccines.
Collapse
Affiliation(s)
- Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- * E-mail:
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alberto Zampiero
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Bianchini
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giada Di Pietro
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessia Scala
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Raffaella Pinzani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Emilio Fossali
- Emergency Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Section of Microbiology, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Nicola Principi
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| |
Collapse
|
63
|
Functional Analysis of the 60-Nucleotide Duplication in the Respiratory Syncytial Virus Buenos Aires Strain Attachment Glycoprotein. J Virol 2015; 89:8258-66. [PMID: 26018171 DOI: 10.1128/jvi.01045-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/25/2015] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED There are two subgroups of respiratory syncytial virus (RSV), A and B, and within each subgroup, isolates are further divided into clades. Several years ago, multiple subgroup B isolates which contained a duplication of 60 nucleotides in the glycoprotein (G) gene were described. These isolates were given a new clade designation of BA based on the site of isolation, Buenos Aires, Argentina. BA RSV strains have since become the predominant circulating clade of RSV B viruses. We hypothesized that the duplicated region in G serves to enhance the function of G in the virus life cycle. We generated recombinant viruses that express a consensus BA G gene or a consensus BA G gene lacking the duplication (GΔdup). We determined that the duplicated region functions during virus attachment to cells. Additionally, we showed that in vitro, the virus containing the duplication has a fitness advantage compared to the virus without the duplication. Our data demonstrate that the duplicated region in the BA strain G protein augments virus attachment and fitness. IMPORTANCE Respiratory syncytial virus (RSV) is an important pathogen for infants for which there is no vaccine. Different strains of RSV circulate from year to year, and the predominating strains change over time. Subgroup B RSV strains with a duplication in the attachment glycoprotein (G) emerged and then became the dominant B genotype. We found that a recombinant virus harboring the duplication bound more efficiently to cells and was more fit than a recombinant strain lacking the duplication. Our work advances a mechanism for an important natural RSV mutation.
Collapse
|
64
|
Molecular epidemiology and molecular characterization of respiratory syncytial viruses at a tertiary care university hospital in Catalonia (Spain) during the 2013–2014 season. J Clin Virol 2015; 66:27-32. [DOI: 10.1016/j.jcv.2015.02.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/22/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023]
|
65
|
Cui G, Zhu R, Deng J, Zhao L, Sun Y, Wang F, Qian Y. Rapid replacement of prevailing genotype of human respiratory syncytial virus by genotype ON1 in Beijing, 2012-2014. INFECTION GENETICS AND EVOLUTION 2015; 33:163-8. [PMID: 25929164 DOI: 10.1016/j.meegid.2015.04.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/15/2015] [Accepted: 04/26/2015] [Indexed: 11/19/2022]
Abstract
Human respiratory syncytial virus (HRSV) is the most common viral pathogen causing lower respiratory infections in infants and young children worldwide. HRSV ON1 genotype in subgroup A with a characteristic of a 72 nucleotide duplication in the second highly variable region of attachment glycoprotein gene, has been reported in some countries since it was first detected in clinical samples collected in Canada in 2010. In this study, 557 HRSV antigen-positive nasopharyngeal aspirates were randomly selected during 2012/2013 to 2013/2014 HRSV seasons in Beijing for subgroup typing and for ON1 genotype screening by using a PCR based method developed for easily identifying genotype ON1 out of strains of subtype A. It was found that subgroup B was dominant in the 2012/2013 season and sudden shift of subgroup dominance from B to A and rapid replacement of previously prevailing NA1 genotype by ON1 genotype occurred in the 2013/2014 season. Reversible amino acid replacement in the G protein gene was found in a new branch of ON1 genotype. The evolutionary rate of the 351 global ON1 sequences was estimated to 7.34 × 10(-3) nucleotide substitutions per site per year (95% highest probability density intervals, HPD, 5.71 × 10(-3) to 9.04 × 10(-3)), with the time of most recent common ancestor dating back to June 2009.
Collapse
Affiliation(s)
- Guanglin Cui
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Runan Zhu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Jie Deng
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Linqing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Yu Sun
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Fang Wang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China
| | - Yuan Qian
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, 2 Yabao Road, Beijing 100020, China.
| |
Collapse
|
66
|
Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. J Virol 2015; 89:3444-54. [PMID: 25609811 PMCID: PMC4403408 DOI: 10.1128/jvi.03391-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is associated with severe childhood respiratory infections. A clear description of local RSV molecular epidemiology, evolution, and transmission requires detailed sequence data and can inform new strategies for virus control and vaccine development. We have generated 27 complete or nearly complete genomes of RSV from hospitalized children attending a rural coastal district hospital in Kilifi, Kenya, over a 10-year period using a novel full-genome deep-sequencing process. Phylogenetic analysis of the new genomes demonstrated the existence and cocirculation of multiple genotypes in both RSV A and B groups in Kilifi. Comparison of local versus global strains demonstrated that most RSV A variants observed locally in Kilifi were also seen in other parts of the world, while the Kilifi RSV B genomes encoded a high degree of variation that was not observed in other parts of the world. The nucleotide substitution rates for the individual open reading frames (ORFs) were highest in the regions encoding the attachment (G) glycoprotein and the NS2 protein. The analysis of RSV full genomes, compared to subgenomic regions, provided more precise estimates of the RSV sequence changes and revealed important patterns of RSV genomic variation and global movement. The novel sequencing method and the new RSV genomic sequences reported here expand our knowledge base for large-scale RSV epidemiological and transmission studies. IMPORTANCE The new RSV genomic sequences and the novel sequencing method reported here provide important data for understanding RSV transmission and vaccine development. Given the complex interplay between RSV A and RSV B infections, the existence of local RSV B evolution is an important factor in vaccine deployment.
Collapse
|
67
|
Hirano E, Kobayashi M, Tsukagoshi H, Yoshida LM, Kuroda M, Noda M, Ishioka T, Kozawa K, Ishii H, Yoshida A, Oishi K, Ryo A, Kimura H. Molecular evolution of human respiratory syncytial virus attachment glycoprotein (G) gene of new genotype ON1 and ancestor NA1. INFECTION GENETICS AND EVOLUTION 2014; 28:183-91. [DOI: 10.1016/j.meegid.2014.09.030] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
|
68
|
Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol 2014; 15:538. [PMID: 25418119 PMCID: PMC4282151 DOI: 10.1186/s13059-014-0538-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local transmission and global spread. The analyses of these data have implications for all levels of clinical and public health practice, from institutional infection control to policies for surveillance, prevention and treatment. This review highlights the range of epidemiological questions that can be addressed from the combination of genome sequence and traditional ‘line lists’ (tables of epidemiological data where each line includes demographic and clinical features of infected individuals). We identify opportunities for these data to inform interventions that reduce disease incidence and prevalence. By considering current limitations of, and challenges to, interpreting these data, we aim to outline a research agenda to accelerate the genomics-driven transformation in public health microbiology.
Collapse
|
69
|
Tabatabai J, Prifert C, Pfeil J, Grulich-Henn J, Schnitzler P. Novel respiratory syncytial virus (RSV) genotype ON1 predominates in Germany during winter season 2012-13. PLoS One 2014; 9:e109191. [PMID: 25290155 PMCID: PMC4188618 DOI: 10.1371/journal.pone.0109191] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 08/29/2014] [Indexed: 11/19/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of hospitalization especially in young children with respiratory tract infections (RTI). Patterns of circulating RSV genotypes can provide a better understanding of the molecular epidemiology of RSV infection. We retrospectively analyzed the genetic diversity of RSV infection in hospitalized children with acute RTI admitted to University Hospital Heidelberg/Germany between October 2012 and April 2013. Nasopharyngeal aspirates (NPA) were routinely obtained in 240 children younger than 2 years of age who presented with clinical symptoms of upper or lower RTI. We analyzed NPAs via PCR and sequence analysis of the second variable region of the RSV G gene coding for the attachment glycoprotein. We obtained medical records reviewing routine clinical data. RSV was detected in 134/240 children. In RSV-positive patients the most common diagnosis was bronchitis/bronchiolitis (75.4%). The mean duration of hospitalization was longer in RSV-positive compared to RSV-negative patients (3.5 vs. 5.1 days; p<0.01). RSV-A was detected in 82.1%, RSV-B in 17.9% of all samples. Phylogenetic analysis of 112 isolates revealed that the majority of RSV-A strains (65%) belonged to the novel ON1 genotype containing a 72-nucleotide duplication. However, genotype ON1 was not associated with a more severe course of illness when taking basic clinical/laboratory parameters into account. Molecular characterization of RSV confirms the co-circulation of multiple genotypes of subtype RSV-A and RSV-B. The duplication in the G gene of genotype ON1 might have an effect on the rapid spread of this emerging RSV strain.
Collapse
Affiliation(s)
- Julia Tabatabai
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christiane Prifert
- Institute of Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Johannes Pfeil
- Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
- German Centre for Infectious Diseases (DZIF), Heidelberg, Germany
| | | | - Paul Schnitzler
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
- * E-mail:
| |
Collapse
|
70
|
Avadhanula V, Chemaly RF, Shah DP, Ghantoji SS, Azzi JM, Aideyan LO, Mei M, Piedra PA. Infection with novel respiratory syncytial virus genotype Ontario (ON1) in adult hematopoietic cell transplant recipients, Texas, 2011-2013. J Infect Dis 2014; 211:582-9. [PMID: 25156562 DOI: 10.1093/infdis/jiu473] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) can cause severe respiratory disease in adult hematopoietic cell transplant (HCT) recipients. RSV subgroups A and B have evolved into multiple genotypes. We report on a recently described RSV genotype (ON1) in a cohort of adult HCT recipients in Texas. METHODS Twenty adult HCT recipients were enrolled as a part of an efficacy trial of ribavirin therapy. RSV identification and genotyping was performed using molecular techniques. RSV-specific neutralizing antibody (NAb) responses were measured. RESULTS ON1 genotype was detected in 3 of 6 patients in the 2011-2012 season and in 8 of 14 patients in 2012-2013 season. Other genotypes detected were NA1 and BA. NAb levels were low at enrollment. Eight of 9 patients who cleared the RSV infection within 2 weeks mounted a ≥4-fold NAb response, compared with 2 of 8 who shed the virus for >2 weeks. The clinical course of those infected with ON1 was comparable to the course for individuals infected with other genotypes. CONCLUSION This is the first report of RSV ON1 genotype in the United States, and ON1 genotype was dominant genotype in adult HCT recipients. Interestingly, faster viral clearance was associated with a ≥4-fold NAb response, likely indicating a reconstituted immune system.
Collapse
Affiliation(s)
| | - Roy F Chemaly
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dimpy P Shah
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shashank S Ghantoji
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jacques M Azzi
- Departments of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Minghua Mei
- Department of Molecular Virology and Microbiology
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology Department of Pediatrics, Baylor College of Medicine
| |
Collapse
|
71
|
The genetic variability of glycoproteins among respiratory syncytial virus subtype A in China between 2009 and 2013. INFECTION GENETICS AND EVOLUTION 2014; 27:339-47. [PMID: 25109878 DOI: 10.1016/j.meegid.2014.07.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 11/21/2022]
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections in infants and children under 5years of age. The novel genotype ON1 has a 72-nucleotide duplication, which is the largest duplicated genome portion of RSV. Whether the ON1 genotype will follow the pattern of the BA genotype, which has a 60-nucleotide duplication, and become the predominant RSV-A strain is a global concern. To obtain information regarding the prevalence of the ON1 genotype in Chongqing in Southwestern China, we examined the circulation pattern of RSV-A identified over four consecutive years (June 2009 to August 2013). In this study, 312 (12%) RSV-A strains were isolated from 2601 nasopharyngeal aspirates, and partial G gene was sequenced successfully in 250 isolates. Of the sequenced Chongqing RSV-A isolates, 237 (94.8%) strains were the NA1 genotype, 4 (1.6%) strains were the NA3 genotype, 4 (1.6%) strains were the NA4 genotype, 1 (0.4%) strain was the GA1 genotype, and 4 (1.6%) strains were identified as the ON1 genotype. Analysis of the distribution, phylogeny, and evolution of the ON1 strains that were collected globally until December 2013 revealed that the ON1 genotype has rapidly disseminated across the world under positive selection pressures. Future studies will determine whether this new genotype will continue to spread and become the dominant strain of RSV-A worldwide. These findings may contribute to the understanding of RSV evolution and to the potential development of a vaccine against RSV.
Collapse
|