The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus

Abstract Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been extensively studied for respiratory viruses such as seasonal influenza, and more recent...

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Main Authors: Annefleur C. Langedijk, Bram Vrancken, Robert Jan Lebbink, Deidre Wilkins, Elizabeth J. Kelly, Eugenio Baraldi, Abiel Homero Mascareñas de Los Santos, Daria M. Danilenko, Eun Hwa Choi, María Angélica Palomino, Hsin Chi, Christian Keller, Robert Cohen, Jesse Papenburg, Jeffrey Pernica, Anne Greenough, Peter Richmond, Federico Martinón-Torres, Terho Heikkinen, Renato T. Stein, Mitsuaki Hosoya, Marta C. Nunes, Charl Verwey, Anouk Evers, Leyla Kragten-Tabatabaie, Marc A. Suchard, Sergei L. Kosakovsky Pond, Chiara Poletto, Vittoria Colizza, Philippe Lemey, Louis J. Bont, on behalf of the INFORM-RSV Study Group
Format: Article
Language:English
Published: Nature Portfolio 2024-04-01
Series:Nature Communications
Online Access:https://doi.org/10.1038/s41467-024-47118-6
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author Annefleur C. Langedijk
Bram Vrancken
Robert Jan Lebbink
Deidre Wilkins
Elizabeth J. Kelly
Eugenio Baraldi
Abiel Homero Mascareñas de Los Santos
Daria M. Danilenko
Eun Hwa Choi
María Angélica Palomino
Hsin Chi
Christian Keller
Robert Cohen
Jesse Papenburg
Jeffrey Pernica
Anne Greenough
Peter Richmond
Federico Martinón-Torres
Terho Heikkinen
Renato T. Stein
Mitsuaki Hosoya
Marta C. Nunes
Charl Verwey
Anouk Evers
Leyla Kragten-Tabatabaie
Marc A. Suchard
Sergei L. Kosakovsky Pond
Chiara Poletto
Vittoria Colizza
Philippe Lemey
Louis J. Bont
on behalf of the INFORM-RSV Study Group
author_facet Annefleur C. Langedijk
Bram Vrancken
Robert Jan Lebbink
Deidre Wilkins
Elizabeth J. Kelly
Eugenio Baraldi
Abiel Homero Mascareñas de Los Santos
Daria M. Danilenko
Eun Hwa Choi
María Angélica Palomino
Hsin Chi
Christian Keller
Robert Cohen
Jesse Papenburg
Jeffrey Pernica
Anne Greenough
Peter Richmond
Federico Martinón-Torres
Terho Heikkinen
Renato T. Stein
Mitsuaki Hosoya
Marta C. Nunes
Charl Verwey
Anouk Evers
Leyla Kragten-Tabatabaie
Marc A. Suchard
Sergei L. Kosakovsky Pond
Chiara Poletto
Vittoria Colizza
Philippe Lemey
Louis J. Bont
on behalf of the INFORM-RSV Study Group
author_sort Annefleur C. Langedijk
collection DOAJ
description Abstract Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been extensively studied for respiratory viruses such as seasonal influenza, and more recently also in great detail for SARS-CoV-2, a lack of global multi-annual sampling of complete RSV genomes limits our understanding of RSV molecular epidemiology. Here, we capitalise on the genomic surveillance by the INFORM-RSV study and apply phylodynamic approaches to uncover how selection and neutral epidemiological processes shape RSV diversity. Using complete viral genome sequences, we show similar patterns of site-specific diversifying selection among RSVA and RSVB and recover the imprint of non-neutral epidemic processes on their genealogies. Using a phylogeographic approach, we provide evidence for air travel governing the global patterns of RSVA and RSVB spread, which results in a considerable degree of phylogenetic mixing across countries. Our findings highlight the potential of systematic global RSV genomic surveillance for transforming our understanding of global RSV spread.
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spelling doaj.art-45e7038869c54007951a43a1f120bf0b2024-04-14T11:20:58ZengNature PortfolioNature Communications2041-17232024-04-0115111210.1038/s41467-024-47118-6The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virusAnnefleur C. Langedijk0Bram Vrancken1Robert Jan Lebbink2Deidre Wilkins3Elizabeth J. Kelly4Eugenio Baraldi5Abiel Homero Mascareñas de Los Santos6Daria M. Danilenko7Eun Hwa Choi8María Angélica Palomino9Hsin Chi10Christian Keller11Robert Cohen12Jesse Papenburg13Jeffrey Pernica14Anne Greenough15Peter Richmond16Federico Martinón-Torres17Terho Heikkinen18Renato T. Stein19Mitsuaki Hosoya20Marta C. Nunes21Charl Verwey22Anouk Evers23Leyla Kragten-Tabatabaie24Marc A. Suchard25Sergei L. Kosakovsky Pond26Chiara Poletto27Vittoria Colizza28Philippe Lemey29Louis J. Bont30on behalf of the INFORM-RSV Study GroupDepartment of Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Centre UtrechtDepartment of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological VirologyDepartment of Medical Microbiology, University Medical Center UtrechtTranslational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZenecaTranslational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZenecaDepartment of Woman’s and Child’s Health, University Hospital of PadovaJose Eluterio Gonzalez Hospital UniversitarioSmorodintsev Research Institute of InfluenzaSeoul National University Children’s HospitalHospital Roberto del Río, Universidad de ChileMacKay Children’s HospitalInstitute of Virology, University Hospital Giessen and MarburgUniversité Paris XIIMcGill University Health CentreMcMaster UniversityReSViNET FoundationUniversity of Western AustraliaReSViNET FoundationReSViNET FoundationReSViNET FoundationFukushima Medical University School of MedicineReSViNET FoundationDepartment of Paediatrics and Child Health, Faculty of Health Sciences, University of the WitwatersrandDepartment of Medical Microbiology, University Medical Center UtrechtReSViNET FoundationDepartment of Human Genetics, David Geffen School of Medicine, University of CaliforniaInstitute for Genomics and Evolutionary Medicine, Department of Biology, Temple UniversityINSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESPINSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESPDepartment of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological VirologyDepartment of Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Centre UtrechtAbstract Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been extensively studied for respiratory viruses such as seasonal influenza, and more recently also in great detail for SARS-CoV-2, a lack of global multi-annual sampling of complete RSV genomes limits our understanding of RSV molecular epidemiology. Here, we capitalise on the genomic surveillance by the INFORM-RSV study and apply phylodynamic approaches to uncover how selection and neutral epidemiological processes shape RSV diversity. Using complete viral genome sequences, we show similar patterns of site-specific diversifying selection among RSVA and RSVB and recover the imprint of non-neutral epidemic processes on their genealogies. Using a phylogeographic approach, we provide evidence for air travel governing the global patterns of RSVA and RSVB spread, which results in a considerable degree of phylogenetic mixing across countries. Our findings highlight the potential of systematic global RSV genomic surveillance for transforming our understanding of global RSV spread.https://doi.org/10.1038/s41467-024-47118-6
spellingShingle Annefleur C. Langedijk
Bram Vrancken
Robert Jan Lebbink
Deidre Wilkins
Elizabeth J. Kelly
Eugenio Baraldi
Abiel Homero Mascareñas de Los Santos
Daria M. Danilenko
Eun Hwa Choi
María Angélica Palomino
Hsin Chi
Christian Keller
Robert Cohen
Jesse Papenburg
Jeffrey Pernica
Anne Greenough
Peter Richmond
Federico Martinón-Torres
Terho Heikkinen
Renato T. Stein
Mitsuaki Hosoya
Marta C. Nunes
Charl Verwey
Anouk Evers
Leyla Kragten-Tabatabaie
Marc A. Suchard
Sergei L. Kosakovsky Pond
Chiara Poletto
Vittoria Colizza
Philippe Lemey
Louis J. Bont
on behalf of the INFORM-RSV Study Group
The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
Nature Communications
title The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
title_full The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
title_fullStr The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
title_full_unstemmed The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
title_short The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
title_sort genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
url https://doi.org/10.1038/s41467-024-47118-6
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