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Jelley L, Douglas J, O'Neill M, Berquist K, Claasen A, Wang J, Utekar S, Johnston H, Judy B, Allais M, de Ligt J, Tan CE, Seeds R, Wood T, Aminisani N, Jennings T, Welch D, Turner N, McIntyre P, Dowell T, Trenholme A, Byrnes C, Webby R, French N, Winter D, Huang QS, Geoghegan JL. Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24310412. [PMID: 39072023 PMCID: PMC11275701 DOI: 10.1101/2024.07.15.24310412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.
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Haider SA, Jamal Z, Tahir F, Salman M, Umair M. Genomic characterization of human respiratory syncytial virus circulating in Islamabad, Pakistan, during an outbreak in 2022-2023. Arch Virol 2024; 169:106. [PMID: 38644429 DOI: 10.1007/s00705-024-06036-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/26/2024] [Indexed: 04/23/2024]
Abstract
In this study, conducted at the National Institute of Health, Islamabad, during an outbreak of human respiratory syncytial virus (hRSV) from December 2022 to January 2023, the first whole-genome sequences of hRSV isolates from Islamabad, Pakistan, were determined. Out of 10 positive samples, five were sequenced, revealing the presence of two genotypes: RSV-A (GA2.3.5, ON1 strain) and RSV-B (GB5.0.5.a, BA-10 strain). A rare non-synonymous substitution (E232G) in G the protein and N276S in the F protein were found in RSV-A. In RSV-B, the unique mutations K191R, Q209R, and I206M were found in the F protein. These mutations could potentially influence vaccine efficacy and viral pathogenicity. This research underscores the importance of genomic surveillance for understanding RSV diversity and guiding public health responses in Pakistan.
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Affiliation(s)
- Syed Adnan Haider
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Zunera Jamal
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Faheem Tahir
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Massab Umair
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan.
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3
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Iglesias-Caballero M, Camarero-Serrano S, Varona S, Mas V, Calvo C, García ML, García-Costa J, Vázquez-Morón S, Monzón S, Campoy A, Cuesta I, Pozo F, Casas I. Genomic characterisation of respiratory syncytial virus: a novel system for whole genome sequencing and full-length G and F gene sequences. Euro Surveill 2023; 28:2300637. [PMID: 38062945 PMCID: PMC10831411 DOI: 10.2807/1560-7917.es.2023.28.49.2300637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
To advance our understanding of respiratory syncytial virus (RSV) impact through genomic surveillance, we describe two PCR-based sequencing systems, (i) RSVAB-WGS for generic whole-genome sequencing and (ii) RSVAB-GF, which targets major viral antigens, G and F, and is used as a complement for challenging cases with low viral load. These methods monitor RSV genetic diversity to inform molecular epidemiology, vaccine effectiveness and treatment strategies, contributing also to the standardisation of surveillance in a new era of vaccines.
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Affiliation(s)
- María Iglesias-Caballero
- Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- These authors contributed equally
| | - Sara Camarero-Serrano
- Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Sarai Varona
- Bioinformatics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Vicente Mas
- Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Cristina Calvo
- Paediatric Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Hospital La Paz Institute for Health Research (IdiPAZ Foundation), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - María Luz García
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
- Paediatric Department, Severo Ochoa University Hospital, Leganés, Biomedical Sciences Research Institute, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain
| | | | - Sonia Vázquez-Morón
- Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Albert Campoy
- Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Isabel Cuesta
- Bioinformatics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Francisco Pozo
- Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
| | - Inmaculada Casas
- Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
- These authors contributed equally
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4
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Pangesti KNA, Ansari HR, Bayoumi A, Kesson AM, Hill-Cawthorne GA, Abd El Ghany M. Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia. Microb Genom 2023; 9:001095. [PMID: 37656160 PMCID: PMC10569731 DOI: 10.1099/mgen.0.001095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
Respiratory syncytial virus (RSV), or human orthopneumovirus, is a major cause of acute lower respiratory infection (ALRI), particularly in young children, causing significant morbidity and mortality. We used pathogen genomics to characterize the population structure and genetic signatures of RSV isolates circulating in children in New South Wales between 2016 and 2018 and to understand the evolutionary dynamics of these strains in the context of publicly available RSV genomes from the region and globally. Whole-genome phylogenetic analysis demonstrated the co-circulation of a few major RSV clades in the paediatric population from Sydney. The whole-genome-based genotypes A23 (RSV-A ON1-like genotype) and B6 (RSV-B BA9-like genotype) were the predominant RSV-A and RSV-B genotypes circulating during the study period, respectively. These genotypes were characterized with high levels of diversity of predicted N- and O-linked glycosylation patterns in both the G and F glycoproteins. Interestingly, a novel 72-nucleotide triplication in the sequence that corresponds to the C-terminal region of the G gene was identified in four of the A23 genotype sequenced in this study. Consistently, the population dynamics analysis demonstrated a continuous increase in the effective population size of A23 and B6 genotypes globally. Further investigations including functional mapping of mutations and identifying the impact of sequence changes on virus fitness are highly required. This study highlights the potential impact of an integrated approach that uses WG-based phylogeny and studying selective pressure events in understanding the emergence and dissemination of RSV genotypes.
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Affiliation(s)
- Krisna N. A. Pangesti
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Hifzur R. Ansari
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Ali Bayoumi
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Alison M. Kesson
- Department of Infectious Diseases and Microbiology, The Children’s Hospital at Westmead, Sydney, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, Australia
| | - Grant A. Hill-Cawthorne
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Moataz Abd El Ghany
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- The Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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5
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Shishir TA, Saha O, Rajia S, Mondol SM, Masum MHU, Rahaman MM, Hossen F, Bahadur NM, Ahmed F, Naser IB, Amin MR. Genome-wide study of globally distributed respiratory syncytial virus (RSV) strains implicates diversification utilizing phylodynamics and mutational analysis. Sci Rep 2023; 13:13531. [PMID: 37598270 PMCID: PMC10439963 DOI: 10.1038/s41598-023-40760-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a common respiratory pathogen that causes mild cold-like symptoms and severe lower respiratory tract infections, causing hospitalizations in children, the elderly and immunocompromised individuals. Due to genetic variability, this virus causes life-threatening pneumonia and bronchiolitis in young infants. Thus, we examined 3600 whole genome sequences submitted to GISAID by 31 December 2022 to examine the genetic variability of RSV. While RSVA and RSVB coexist throughout RSV seasons, RSVA is more prevalent, fatal, and epidemic-prone in several countries, including the United States, the United Kingdom, Australia, and China. Additionally, the virus's attachment glycoprotein and fusion protein were highly mutated, with RSVA having higher Shannon entropy than RSVB. The genetic makeup of these viruses contributes significantly to their prevalence and epidemic potential. Several strain-specific SNPs co-occurred with specific haplotypes of RSVA and RSVB, followed by different haplotypes of the viruses. RSVA and RSVB have the highest linkage probability at loci T12844A/T3483C and G13959T/C2198T, respectively. The results indicate that specific haplotypes and SNPs may significantly affect their spread. Overall, this analysis presents a promising strategy for tracking the evolving epidemic situation and genetic variants of RSV, which could aid in developing effective control, prophylactic, and treatment strategies.
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Affiliation(s)
- Tushar Ahmed Shishir
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Otun Saha
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh.
| | - Sultana Rajia
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Md Habib Ullah Masum
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Foysal Hossen
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Firoz Ahmed
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Iftekhar Bin Naser
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Mohammad Ruhul Amin
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh.
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Yan Y, Wang D, Li Y, Wu Z, Liu H, Shi Y, Lu X, Liu D. Prevalence, variation, and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei, China during 2020-2021. Virol Sin 2023; 38:363-372. [PMID: 37146717 PMCID: PMC10311268 DOI: 10.1016/j.virs.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/26/2023] [Indexed: 05/07/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a severe threat to children and a main cause of acute lower respiratory tract infections. Nevertheless, the intra-host evolution and inter-regional diffusion of RSV are little known. In this study, we performed a systematic surveillance in hospitalized children in Hubei during 2020-2021, in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing (mNGS). RSV-A and RSV-B groups co-circulated during surveillance with RSV-B being predominant. About 46 high-quality genomes were used for further analyses. A total of 163 intra-host nucleotide variation (iSNV) sites distributed in 34 samples were detected, and glycoprotein (G) gene was the most enriched gene for iSNVs, with non-synonymous substitutions more than synonymous substitutions. Evolutionary dynamic analysis showed that the evolutionary rates of G and NS2 genes were higher, and the population size of RSV groups changed over time. We also found evidences of inter-regional diffusion from Europe and Oceania to Hubei for RSV-A and RSV-B, respectively. This study highlighted the intra-host and inter-host evolution of RSV, and provided some evidences for understanding the evolution of RSV.
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Affiliation(s)
- Yi Yan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, 430071, China; Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Decheng Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, 430071, China; Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ying Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, 430071, China; Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 101408, China; Department of Respiratory Medicine, Wuhan Children' Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China; Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Zhiyong Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, 430071, China; Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Haizhou Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, 430071, China; Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yue Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, 430071, China; Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiaoxia Lu
- Department of Respiratory Medicine, Wuhan Children' Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China; Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China.
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan, 430071, China; Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 101408, China.
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Stiboy E, Chan M, Islam MS, Saravanos GL, Lui K, Jaffe A, Homaira N. Variation in clinical practice guidelines for use of palivizumab in preventing severe respiratory syncytial viral (RSV) disease in high-risk infants. Pediatr Pulmonol 2023; 58:1210-1220. [PMID: 36748923 DOI: 10.1002/ppul.26324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 02/08/2023]
Abstract
BACKGROUND Uniformity and compliance with clinical practice guidelines (CPGs) for use of palivizumab in preventing severe respiratory syncytial viral infection in Australian high-risk infants remain unclear. METHODS An online survey was conducted across the Australian and New Zealand Neonatal Network (ANZNN) to determine clinical practices around palivizumab. A literature search was also performed to identify and compare national and international guidelines. RESULTS A total of 65 of 422 ANZNN members completed the survey. Respondents included 61 senior medical staff of consultants/staff specialists (78%) and four nursing staff (6%). According to the survey, infants most likely to be recommended palivizumab included preterm infants born <29 weeks gestational age (GA) (30%), children with chronic lung diseases (CLDs) born <32 weeks GA (40%), and with hemodynamically significant heart disease (35%). Many of the respondents (53%) stated that CPGs for palivizumab were developed locally. Literature search identified 20 guidelines (10 international and 10 domestic); 16 (80%) recommended palivizumab use in preterm infants, 16 (80%) recommended use in infants with CLD, 17 (85%) in congenital heart disease and 6 (30%) in bronchopulmonary dysplasia (BPD). Eight (40%) guidelines provided specific recommendations for immunocompromised infants. Canada, Western Australia, and American Academy of Paediatrics provided recommendations for Indigenous children. Frequency and dosage of palivizumab was universal across all CPGs. None of the international guidelines obtained were from low- or middle-income countries. CONCLUSIONS Standardization of CPGs may improve clinical decision making around use of palivizumab in high-risk infants.
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Affiliation(s)
- Eunice Stiboy
- School of Public Health, The University of Sydney, Camperdown, Australia
| | - Mei Chan
- UNSW Medicine and Health, Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia
| | - Md Saiful Islam
- National Center for Epidemiology and Population Health, ANU, Canberra, Australia
| | - Gemma L Saravanos
- Chidlren's Hospital Westmead Clinical School, The University of Sydney, Camperdown, Australia.,Susan Wakil School of Nursing and Midwifery, The University of Sydney, Camperdown, Australia
| | - Kei Lui
- UNSW Medicine and Health, Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia.,Australian and New Zealand Neonatal Network, UNSW, Sydney, Sydney, Australia.,Deaprtment of Newborn, The Royal Hospital for Women, Randwick, Australia
| | - Adam Jaffe
- UNSW Medicine and Health, Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia.,Respiratory Department, The Sydney Children's Hospital, Randwick, Australia
| | - Nusrat Homaira
- UNSW Medicine and Health, Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia.,Respiratory Department, The Sydney Children's Hospital, Randwick, Australia
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Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia. Pathogens 2022; 11:pathogens11070758. [PMID: 35890000 PMCID: PMC9315832 DOI: 10.3390/pathogens11070758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/13/2022] [Accepted: 06/25/2022] [Indexed: 01/27/2023] Open
Abstract
Human orthopneumovirus (HRSV) is a virus belonging to the Pneumovirus genus that causes lower respiratory tract infections (LRTI) in infants worldwide. In Tunisia, thousands of infants hospitalized for LRTI are found to be positive for HRSV but no whole genome sequences of HRSV strains circulating in this country are available thus far. In this study, five nasal swab samples collected at different time points from a three-month-old female baby with severe immunodeficiency that was hospitalized for acute bronchiolitis were investigated by next generation sequencing. The Tunisian sequences from this study originated from samples collected in 2021, belong to the ON1 genotype of HRSV-A, and are clustered with European sequences from 2019 and not from 2020 or 2021. This is most likely related to local region-specific transmission of different HRSV-A variants due to the COVID-19 related travel restrictions. Overall, this is the first report describing the whole genome sequence of HRSV from Tunisia. However, more sequence data is needed to better understand the genetic diversity and transmission dynamic of HRSV.
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9
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Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nat Commun 2022; 13:2884. [PMID: 35610217 PMCID: PMC9130497 DOI: 10.1038/s41467-022-30485-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is an important cause of acute respiratory infection with the most severe disease in the young and elderly. Non-pharmaceutical interventions and travel restrictions for controlling COVID-19 have impacted the circulation of most respiratory viruses including RSV globally, particularly in Australia, where during 2020 the normal winter epidemics were notably absent. However, in late 2020, unprecedented widespread RSV outbreaks occurred, beginning in spring, and extending into summer across two widely separated regions of the Australian continent, New South Wales (NSW) and Australian Capital Territory (ACT) in the east, and Western Australia. Through genomic sequencing we reveal a major reduction in RSV genetic diversity following COVID-19 emergence with two genetically distinct RSV-A clades circulating cryptically, likely localised for several months prior to an epidemic surge in cases upon relaxation of COVID-19 control measures. The NSW/ACT clade subsequently spread to the neighbouring state of Victoria and to cause extensive outbreaks and hospitalisations in early 2021. These findings highlight the need for continued surveillance and sequencing of RSV and other respiratory viruses during and after the COVID-19 pandemic, as mitigation measures may disrupt seasonal patterns, causing larger or more severe outbreaks. Non-pharmaceutical interventions for COVID-19 also reduced incidence of respiratory pathogens such as respiratory syncytial virus (RSV). Here, the authors report the resurgence of RSV in Australia following lifting of some of the restrictions and describe reduction in genetic diversity in circulating clades.
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10
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Lee CY, Fang YP, Wang LC, Chou TY, Liu HF. Genetic Diversity and Molecular Epidemiology of Circulating Respiratory Syncytial Virus in Central Taiwan, 2008-2017. Viruses 2021; 14:v14010032. [PMID: 35062237 PMCID: PMC8777914 DOI: 10.3390/v14010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/22/2022] Open
Abstract
In this study, we investigated the molecular evolution and phylodynamics of respiratory syncytial virus (RSV) over 10 consecutive seasons (2008–2017) and the genetic variability of the RSV genotypes ON1 and BA in central Taiwan. The ectodomain region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the second hypervariable region of the G protein in RSV ON1 and BA were analyzed. A total of 132 RSV-A and 81 RSV-B isolates were obtained. Phylogenetic analysis revealed that the NA1, ON1, and BA9 genotypes were responsible for the RSV epidemics in central Taiwan in the study period. For RSV-A, the NA1 genotype predominated during the 2008–2011 seasons. The ON1 genotype was first detected in 2011 and replaced NA1 after 2012. For RSV-B, the BA9 and BA10 genotypes cocirculated from 2008 to 2010, but the BA9 genotype has predominated since 2012. Amino acid sequence alignments revealed the continuous evolution of the G gene in the ectodomain region. The predicted N-glycosylation sites were relatively conserved in the ON1 (site 237 and 318) and BA9 (site 296 and 310) genotype strains. Our results contribute to the understanding and prediction of the temporal evolution of RSV at the local level.
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Affiliation(s)
- Chun-Yi Lee
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua 505029, Taiwan; (C.-Y.L.); (Y.-P.F.)
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
| | - Yu-Ping Fang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua 505029, Taiwan; (C.-Y.L.); (Y.-P.F.)
| | - Li-Chung Wang
- Department of Pathology and Laboratory Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
| | - Teh-Ying Chou
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, Mackay Memorial Hospital, Taipei 25160, Taiwan
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City 25245, Taiwan
- Correspondence:
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11
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Saito M, Tsukagoshi H, Sada M, Sunagawa S, Shirai T, Okayama K, Sugai T, Tsugawa T, Hayashi Y, Ryo A, Takeda M, Kawashima H, Saruki N, Kimura H. Detailed Evolutionary Analyses of the F Gene in the Respiratory Syncytial Virus Subgroup A. Viruses 2021; 13:v13122525. [PMID: 34960794 PMCID: PMC8706373 DOI: 10.3390/v13122525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/20/2022] Open
Abstract
We performed evolution, phylodynamics, and reinfection-related antigenicity analyses of respiratory syncytial virus subgroup A (RSV-A) fusion (F) gene in globally collected strains (1465 strains) using authentic bioinformatics methods. The time-scaled evolutionary tree using the Bayesian Markov chain Monte Carlo method estimated that a common ancestor of the RSV-A, RSV-B, and bovine-RSV diverged at around 450 years ago, and RSV-A and RSV-B diverged around 250 years ago. Finally, the RSV-A F gene formed eight genotypes (GA1-GA7 and NA1) over the last 80 years. Phylodynamics of RSV-A F gene, including all genotype strains, increased twice in the 1990s and 2010s, while patterns of each RSV-A genotype were different. Phylogenetic distance analysis suggested that the genetic distances of the strains were relatively short (less than 0.05). No positive selection sites were estimated, while many negative selection sites were found. Moreover, the F protein 3D structure mapping and conformational epitope analysis implied that the conformational epitopes did not correspond to the neutralizing antibody binding sites of the F protein. These results suggested that the RSV-A F gene is relatively conserved, and mismatches between conformational epitopes and neutralizing antibody binding sites of the F protein are responsible for the virus reinfection.
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Affiliation(s)
- Mariko Saito
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, Japan; (M.S.); (H.T.); (N.S.)
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, Japan; (M.S.); (H.T.); (N.S.)
| | - Mitsuru Sada
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Soyoka Sunagawa
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Tatsuya Shirai
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka-shi 181-8611, Japan;
| | - Kaori Okayama
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Toshiyuki Sugai
- Division of Nursing Science, Hiroshima University, Hiroshima-shi 734-8551, Japan;
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo-shi 060-8543, Japan;
| | - Yuriko Hayashi
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama-shi 236-0004, Japan;
| | - Makoto Takeda
- Department of Virology, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Japan;
| | - Hisashi Kawashima
- Department of Pediatrics, Tokyo Medical University, Shinjuku-ku 160-0023, Japan;
| | - Nobuhiro Saruki
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, Japan; (M.S.); (H.T.); (N.S.)
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
- Correspondence: ; Tel.: +81-27-388-0336
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12
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Chen J, Qiu X, Avadhanula V, Shepard SS, Kim DK, Hixson J, Piedra PA, Bahl J. Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis. Influenza Other Respir Viruses 2021; 16:492-500. [PMID: 34894077 PMCID: PMC8983899 DOI: 10.1111/irv.12936] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/12/2021] [Accepted: 10/17/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition. METHODS We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances. RESULTS In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored. CONCLUSIONS This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.
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Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Xueting Qiu
- Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Do-Kyun Kim
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - James Hixson
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
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13
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Robertson M, Eden JS, Levy A, Carter I, Tulloch RL, Cutmore EJ, Horsburgh BA, Sikazwe CT, Dwyer DE, Smith DW, Kok J. The spatial-temporal dynamics of respiratory syncytial virus infections across the east-west coasts of Australia during 2016-17. Virus Evol 2021; 7:veab068. [PMID: 34532066 PMCID: PMC8438877 DOI: 10.1093/ve/veab068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 04/19/2021] [Accepted: 07/22/2021] [Indexed: 01/03/2023] Open
Abstract
Respiratory syncytial virus (RSV) is an important human respiratory pathogen. In temperate regions, a distinct seasonality is observed, where peaks of infections typically occur in early winter, often preceding the annual influenza season. Infections are associated with high rates of morbidity and mortality and in some populations exceed that of influenza. Two subtypes, RSV-A and RSV-B, have been described, and molecular epidemiological studies have shown that both viruses mostly co-circulate. This trend also appears to be the case for Australia; however, previous genomic studies have been limited to cases from one Eastern state—New South Wales. As such, the broader spatial patterns and viral traffic networks across the continent are not known. Here, we conducted a whole-genome study of RSV comparing strains across eastern and Western Australia during the period January 2016 to June 2017. In total, 96 new RSV genomes were sequenced, compiled with previously generated data, and examined using a phylodynamic approach. This analysis revealed that both RSV-A and RSV-B strains were circulating, and each subtype was dominated by a single genotype, RSV-A ON1-like and RSV-B BA10-like viruses. Some geographical clustering was evident in strains from both states with multiple distinct sub-lineages observed and relatively low mixing across jurisdictions, suggesting that endemic transmission was likely seeded from imported, unsampled locations. Overall, the RSV phylogenies reflected a complex pattern of interactions across multiple epidemiological scales from fluid virus traffic across global and regional networks to fine-scale local transmission events.
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Affiliation(s)
- Mark Robertson
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Hospital Ave, Nedlands, WA 6009, Australia
| | - Ian Carter
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Rachel L Tulloch
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Elena J Cutmore
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Bethany A Horsburgh
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Chisha T Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine WA, Hospital Ave, Nedlands, WA 6009, Australia
| | - Dominic E Dwyer
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
| | - David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Hospital Ave, Nedlands, WA 6009, Australia
| | - Jen Kok
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
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14
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Molecular epidemiology of respiratory syncytial virus among children and adults in India 2016 to 2018. Virus Genes 2021; 57:489-501. [PMID: 34524602 PMCID: PMC8440155 DOI: 10.1007/s11262-021-01859-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/25/2021] [Indexed: 11/21/2022]
Abstract
Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections among children less than 5 years of age and the elderly. This study intended to determine the circulating genotypes of RSV among severe acute respiratory illness (SARI) cases during the period 2016–2018 in India, among hospitalized acute febrile illness cases of age ranging from 1 to 65 years. Throat/nasopharyngeal swab samples were subjected for testing RSV and subgroups by real-time reverse transcriptase polymerase chain reaction (RT-PCR), further sequencing and phylogenetic analysis were performed for the second hypervariable region of the G gene. RSV-A and B subtypes co-circulated during the years 2016, 2017, and 2018, with RSV-A as the dominant subtype in 2016, and RSV-B as the dominant subgroup in 2017 and 2018. Phylogenetic analysis revealed that the circulating genotypes of RSV were GA2 (16/16), of RSV-A, and GB5 (23/23) of RSV-B in the South, North, and Northeast region of India during the period between 2016 and 2018. Here we report the first study comprising the distribution of RSV-A and B genotypes in the different geographic regions of India among children and adults during the year 2016 to 2018. We also report GA2.3.7 lineage of GA2 genotype for the first time in India to the best of our knowledge.
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15
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Saravanos GL, Ramos I, Britton PN, Wood NJ. Respiratory syncytial virus subtype circulation and associated disease severity at an Australian paediatric referral hospital, 2014-2018. J Paediatr Child Health 2021; 57:1190-1195. [PMID: 33638925 DOI: 10.1111/jpc.15419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 11/28/2022]
Abstract
AIM Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections in children and the development of vaccines to protect at-risk groups is a global priority. The aim of this study was to describe RSV subtype circulation patterns and associated disease severity to inform on potential impact of an RSV-specific prevention strategy. METHODS Single-centre retrospective observational study of children aged <16 years with laboratory-confirmed RSV infection from 2014 to 2018 inclusive. We described the features and frequency of all RSV subtype detections. We selected a random sample of RSV-A and RSV-B cases from each year (n = 200), described demographic and clinical features of these cases, and compared indicators of disease severity between subtypes. RESULTS We identified 3591 RSV detections over a 5-year period and found consistent co-circulation of subtypes with alternating predominance. Demographic and clinical characteristics were similar between children presenting with RSV-A and RSV-B infections. There was no difference in indicators of severity between the subtypes except for paediatric intensive care unit length of stay which was longer in the RSV-B group (3 vs. 5 days, P = 0.006). Respiratory co-infections were more frequent in the RSV-B group (41.8% vs. 27.4%, P = 0.035). When these were excluded there was no longer a detectable difference in paediatric intensive care unit length of stay. CONCLUSIONS We found co-circulation of RSV subtypes and no convincing evidence of a difference in disease severity between subtypes. RSV-specific interventions will need to be equally effective against both RSV-A and RSV-B to have the greatest impact on reducing severe RSV disease in this population.
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Affiliation(s)
- Gemma L Saravanos
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia.,National Centre for Immunisation Research and Surveillance, Sydney, New South Wales, Australia
| | - Isabelle Ramos
- National Centre for Immunisation Research and Surveillance, Sydney, New South Wales, Australia.,School of Medicine, University of Notre Dame Fremantle, Perth, Western Australia, Australia
| | - Philip N Britton
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Nicholas J Wood
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia.,National Centre for Immunisation Research and Surveillance, Sydney, New South Wales, Australia.,Department of General Medicine, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
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16
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Wagatsuma K, Koolhof IS, Shobugawa Y, Saito R. Shifts in the epidemic season of human respiratory syncytial virus associated with inbound overseas travelers and meteorological conditions in Japan, 2014-2017: An ecological study. PLoS One 2021; 16:e0248932. [PMID: 33765037 PMCID: PMC7993830 DOI: 10.1371/journal.pone.0248932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Few studies have examined the effects of inbound overseas travelers and meteorological conditions on the shift in human respiratory syncytial virus (HRSV) season in Japan. This study aims to test whether the number of inbound overseas travelers and meteorological conditions are associated with the onset week of HRSV epidemic season. The estimation of onset week for 46 prefectures (except for Okinawa prefecture) in Japan for 4-year period (2014–2017) was obtained from previous papers based on the national surveillance data. We obtained data on the yearly number of inbound overseas travelers and meteorological (yearly mean temperature and relative humidity) conditions from Japan National Tourism Organization (JNTO) and Japan Meteorological Agency (JMA), respectively. Multi-level mixed-effects linear regression analysis showed that every 1 person (per 100,000 population) increase in number of overall inbound overseas travelers led to an earlier onset week of HRSV epidemic season in the year by 0.02 week (coefficient –0.02; P<0.01). Higher mean temperature and higher relative humidity were also found to contribute to an earlier onset week by 0.30 week (coefficient –0.30; P<0.05) and 0.18 week (coefficient –0.18; P<0.01), respectively. Additionally, models that included the number of travelers from individual countries (Taiwan, South Korea, and China) except Australia showed that both the number of travelers from each country and meteorological conditions contributed to an earlier onset week. Our analysis showed the earlier onset week of HRSV epidemic season in Japan is associated with increased number of inbound overseas travelers, higher mean temperature, and relative humidity. The impact of international travelers on seasonality of HRSV can be further extended to investigations on the changes of various respiratory infectious diseases especially after the coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Keita Wagatsuma
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- * E-mail:
| | - Iain S. Koolhof
- College of Health and Medicine, School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Yugo Shobugawa
- Department of Active Aging, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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17
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An Amplicon-Based Approach for the Whole-Genome Sequencing of Human Metapneumovirus. Viruses 2021; 13:v13030499. [PMID: 33803613 PMCID: PMC8003040 DOI: 10.3390/v13030499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/29/2022] Open
Abstract
Human metapneumovirus (HMPV) is an important cause of upper and lower respiratory tract disease in individuals of all ages. It is estimated that most individuals will be infected by HMPV by the age of five years old. Despite this burden of disease, there remain caveats in our knowledge of global genetic diversity due to a lack of HMPV sequencing, particularly at the whole-genome scale. The purpose of this study was to create a simple and robust approach for HMPV whole-genome sequencing to be used for genomic epidemiological studies. To design our assay, all available HMPV full-length genome sequences were downloaded from the National Center for Biotechnology Information (NCBI) GenBank database and used to design four primer sets to amplify long, overlapping amplicons spanning the viral genome and, importantly, specific to all known HMPV subtypes. These amplicons were then pooled and sequenced on an Illumina iSeq 100 (Illumina, San Diego, CA, USA); however, the approach is suitable to other common sequencing platforms. We demonstrate the utility of this method using a representative subset of clinical samples and examine these sequences using a phylogenetic approach. Here we present an amplicon-based method for the whole-genome sequencing of HMPV from clinical extracts that can be used to better inform genomic studies of HMPV epidemiology and evolution.
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18
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Global Molecular Epidemiology of Respiratory Syncytial Virus from the 2017-2018 INFORM-RSV Study. J Clin Microbiol 2020; 59:JCM.01828-20. [PMID: 33087438 PMCID: PMC7771447 DOI: 10.1128/jcm.01828-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children, resulting in annual epidemics worldwide. INFORM-RSV is a multiyear clinical study designed to describe the global molecular epidemiology of RSV in children under 5 years of age by monitoring temporal and geographical evolution of current circulating RSV strains, F protein antigenic sites, and their relationships with clinical features of RSV disease. During the pilot season (2017–2018), 410 RSV G-F gene sequences were obtained from 476 RSV-positive nasal samples collected from 8 countries (United Kingdom, Spain, The Netherlands, Finland, Japan, Brazil, South Africa, and Australia). Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children, resulting in annual epidemics worldwide. INFORM-RSV is a multiyear clinical study designed to describe the global molecular epidemiology of RSV in children under 5 years of age by monitoring temporal and geographical evolution of current circulating RSV strains, F protein antigenic sites, and their relationships with clinical features of RSV disease. During the pilot season (2017–2018), 410 RSV G-F gene sequences were obtained from 476 RSV-positive nasal samples collected from 8 countries (United Kingdom, Spain, The Netherlands, Finland, Japan, Brazil, South Africa, and Australia). RSV B (all BA9 genotype) predominated over RSV A (all ON1 genotype) globally (69.0% versus 31.0%) and in all countries except South Africa. Geographic clustering patterns highlighted wide transmission and continued evolution with viral spread. Most RSV strains were from infants of <1 year of age (81.2%), males (56.3%), and patients hospitalized for >24 h (70.5%), with no differences in subtype distribution. Compared to 2013 reference sequences, variations at F protein antigenic sites were observed for both RSV A and B strains, with high-frequency polymorphisms at antigenic site Ø (I206M/Q209R) and site V (L172Q/S173L/K191R) in RSV B strains. The INFORM-RSV 2017–2018 pilot season establishes an important molecular baseline of RSV strain distribution and sequence variability with which to track the emergence of new strains and provide an early warning system of neutralization escape variants that may impact transmission or the effectiveness of vaccines and MAbs under development.
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19
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Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia. Genes (Basel) 2020; 11:genes11111323. [PMID: 33182267 PMCID: PMC7695323 DOI: 10.3390/genes11111323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial virus (HRSV) is a main cause of hospital admission for lower respiratory tract infection. In previous studies from Saudi Arabia, higher prevalence of the NA1 genotype in group A was observed from Riyadh and Taif. This study recruited respiratory cases from Jeddah during January to December, 2017. RSV represented 13.4% in the recruited cases with 64% of them belonging to group A and 36% to group B. All group A cases in this study were ON1 type characterized by duplication of 72 nucleotides, 24 amino acids in the C-terminal in the second hypervariable region of the G gene. In addition, for group B all of the cases were clustered under BA9, which had uniquely characterized as duplication of 60 nucleotides in the G protein. Our sequences showed similarity with earlier sequences from Saudi Arabia, Kuwait, Thailand, South Africa, Spain, the USA and Cyprus. Some amino acid substitutions in the investigated sequences would cause a change in potential O-glycosylation and N-glycosylation profiles from prototype ON1. The predominance of the ON1 and BA9 genotype of RSV-A in Jeddah compared to previous Saudi studies showing predominance of the NA1 genotype for group A. This difference in genotype prevalence could be due to fast spread of the ON1 genotype worldwide or due to the flux of travelers through Jeddah during hajj/umrah compared to Riyadh and Taif. This shift in genotype distribution requires continuous surveillance for genetic characterization of circulating respiratory infections including RSV. These findings may contribute to the understanding of RSV evolution and to the potential development of a vaccine against RSV.
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20
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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: 30] [Impact Index Per Article: 7.5] [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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21
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Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray KA, Eden JS, Chang S, Gall M, Draper J, Sim EM, Bachmann NL, Carter I, Basile K, Byun R, O'Sullivan MV, Chen SCA, Maddocks S, Sorrell TC, Dwyer DE, Holmes EC, Kok J, Prokopenko M, Sintchenko V. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nat Med 2020; 26:1398-1404. [PMID: 32647358 DOI: 10.1038/s41591-020-1000-7] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/25/2020] [Indexed: 01/05/2023]
Abstract
In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China1,2. The disease arising from SARS-CoV-2 infection, coronavirus disease 2019 (COVID-19), subsequently spread rapidly causing a worldwide pandemic. Here we examine the added value of near real-time genome sequencing of SARS-CoV-2 in a subpopulation of infected patients during the first 10 weeks of COVID-19 containment in Australia and compare findings from genomic surveillance with predictions of a computational agent-based model (ABM). Using the Australian census data, the ABM generates over 24 million software agents representing the population of Australia, each with demographic attributes of an anonymous individual. It then simulates transmission of the disease over time, spreading from specific infection sources, using contact rates of individuals within different social contexts. We report that the prospective sequencing of SARS-CoV-2 clarified the probable source of infection in cases where epidemiological links could not be determined, significantly decreased the proportion of COVID-19 cases with contentious links, documented genomically similar cases associated with concurrent transmission in several institutions and identified previously unsuspected links. Only a quarter of sequenced cases appeared to be locally acquired and were concordant with predictions from the ABM. These high-resolution genomic data are crucial to track cases with locally acquired COVID-19 and for timely recognition of independent importations once border restrictions are lifted and trade and travel resume.
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Affiliation(s)
- Rebecca J Rockett
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Alicia Arnott
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Connie Lam
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Rosemarie Sadsad
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, New South Wales, Australia
| | - Verlaine Timms
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Karen-Ann Gray
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Virus Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Sheryl Chang
- Centre for Complex Systems, Faculty of Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Jenny Draper
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Eby M Sim
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Nathan L Bachmann
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Roy Byun
- Health Protection NSW, NSW Ministry of Health, Sydney, New South Wales, Australia
| | - Matthew V O'Sullivan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Sharon C-A Chen
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Dominic E Dwyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Jen Kok
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Mikhail Prokopenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia.,Centre for Complex Systems, Faculty of Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia. .,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia. .,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia. .,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.
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22
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Thielen BK, Bye E, Wang X, Maroushek S, Friedlander H, Bistodeau S, Christensen J, Reisdorf E, Shilts MH, Martin K, Como-Sabetti K, Strain AK, Ferrieri P, Lynfield R. Summer Outbreak of Severe RSV-B Disease, Minnesota, 2017 Associated with Emergence of a Genetically Distinct Viral Lineage. J Infect Dis 2020; 222:288-297. [PMID: 32083677 PMCID: PMC7323494 DOI: 10.1093/infdis/jiaa075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 02/16/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) typically causes winter outbreaks in temperate climates. During summer 2017, the Minnesota Department of Health received a report of increased cases of severe RSV-B infection. METHODS We compared characteristics of summer 2017 cases with those of 2014-2018 summers. To understand the genetic relatedness among viruses, we performed high-throughput sequencing of RSV from patients with a spectrum of illness from sites in Minnesota and Wisconsin. RESULTS From May to September 2017, 58 RSV cases (43 RSV-B) were reported compared to 20-29 cases (3-7 RSV-B) during these months in other years. Median age and frequency of comorbidities were similar, but 55% (24/43) were admitted to the ICU in 2017 compared to 12% in preceding 3 years (odds ratio, 4.84, P < .01). Sequencing was performed on 137 specimens from March 2016 to March 2018. Outbreak cases formed a unique clade sharing a single conserved nonsynonymous change in the SH gene. We observed increased cases during the following winter season, when the new lineage was the predominant strain. CONCLUSIONS We identified an outbreak of severe RSV-B disease associated with a new genetic lineage among urban Minnesota children during a time of expected low RSV circulation.
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Affiliation(s)
- Beth K Thielen
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Erica Bye
- Minnesota Department of Health, St Paul, Minnesota, USA
| | - Xiong Wang
- Minnesota Department of Health, St Paul, Minnesota, USA
| | | | | | | | | | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA
| | - Meghan H Shilts
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Karen Martin
- Minnesota Department of Health, St Paul, Minnesota, USA
| | | | - Anna K Strain
- Minnesota Department of Health, St Paul, Minnesota, USA
| | - Patricia Ferrieri
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ruth Lynfield
- Minnesota Department of Health, St Paul, Minnesota, USA
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23
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Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J, Storey M, Ren X, Tulloch R, Basile K, Wells J, Byun R, Gilroy N, O'Sullivan MV, Sintchenko V, Chen SC, Maddocks S, Sorrell TC, Holmes EC, Dwyer DE, Kok J. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol 2020; 6:veaa027. [PMID: 32296544 PMCID: PMC7147362 DOI: 10.1093/ve/veaa027] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.
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Affiliation(s)
- John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Virus Research & Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, PO Box 412, Westmead, NSW 2145, Australia
| | - Rebecca Rockett
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Hossinur Rahman
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Joep de Ligt
- Institute of Environmental Science and Research, Porirua 5240, New Zealand
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Matthew Storey
- Institute of Environmental Science and Research, Porirua 5240, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Porirua 5240, New Zealand
| | - Rachel Tulloch
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Virus Research & Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, PO Box 412, Westmead, NSW 2145, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Jessica Wells
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Roy Byun
- NSW Ministry of Health, North Sydney, NSW 2059, Australia
| | - Nicky Gilroy
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Matthew V O'Sullivan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sharon C Chen
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Virus Research & Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, PO Box 412, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E Dwyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
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24
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Aljabr W, Armstrong S, Rickett NY, Pollakis G, Touzelet O, Cloutman-Green E, Matthews DA, Hiscox JA. High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo. Viruses 2019; 11:v11100926. [PMID: 31658630 PMCID: PMC6832471 DOI: 10.3390/v11100926] [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] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/27/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20-25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions.
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Affiliation(s)
- Waleed Aljabr
- King Fahad Medical City, Research Center, 59046 Riyadh 11525, Saudi Arabia.
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Natasha Y Rickett
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
| | - Olivier Touzelet
- School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
| | | | - David A Matthews
- School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK.
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L3 5RF, UK.
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25
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A Contemporary View of Respiratory Syncytial Virus (RSV) Biology and Strain-Specific Differences. Pathogens 2019; 8:pathogens8020067. [PMID: 31117229 PMCID: PMC6631838 DOI: 10.3390/pathogens8020067] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/01/2019] [Accepted: 05/04/2019] [Indexed: 01/09/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a human respiratory pathogen which remains a leading viral cause of hospitalizations and mortality among infants in their first year of life. Here, we review the biology of RSV, the primary laboratory isolates or strains which have been used to best characterize the virus since its discovery in 1956, and discuss the implications for genetic and functional variations between the established laboratory strains and the recently identified clinical isolates.
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