title: Within-host whole-genome deep sequencing and diversity analysis of human respiratory syncytial virus infection reveals dynamics of genomic diversity in the absence and presence of immune pressure.
abstract: Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract disease in infants and young children and an important respiratory pathogen in the elderly and immunocompromised. While population-wide molecular epidemiology studies have shown multiple cocirculating RSV genotypes and revealed antigenic and genetic change over successive seasons, little is known about the extent of viral diversity over the course of an individual infection, the origins of novel variants, or the effect of immune pressure on viral diversity and potential immune-escape mutations. To investigate viral population diversity in the presence and absence of selective immune pressures, we studied whole-genome deep sequencing of RSV in upper airway samples from an infant with severe combined immune deficiency syndrome and persistent RSV infection. The infection continued over several months before and after bone marrow transplant (BMT) from his RSV-immune father. RSV diversity was characterized in 26 samples obtained over 78 days. Diversity increased after engraftment, as defined by T-cell presence, and populations reflected variation mostly within the G protein, the major surface antigen. Minority populations with known palivizumab resistance mutations emerged after its administration. The viral population appeared to diversify in response to selective pressures, showing a statistically significant growth in diversity in the presence of pressure from immunity. Defining escape mutations and their dynamics will be useful in the design and application of novel therapeutics and vaccines. These data can contribute to future studies of the relationship between within-host and population-wide RSV phylodynamics.
  
  
  OBJECTIVE
  Human RSV is an important cause of respiratory disease in infants, the elderly, and the immunocompromised. RSV circulating in a community appears to change season by season, but the amount of diversity generated during an individual infection and the impact of immunity on this viral diversity has been unclear. To address this question, we described within-host RSV diversity by whole-genome deep sequencing in a unique clinical case of an RSV-infected infant with severe combined immunodeficiency and effectively no adaptive immunity who then gained adaptive immunity after undergoing bone marrow transplantation. We found that viral diversity increased in the presence of adaptive immunity and was primarily within the G protein, the major surface antigen. These data will be useful in designing RSV treatments and vaccines and to help understand the relationship between the dynamics of viral diversification within individual hosts and the viral populations circulating in a community.
authors.affiliation: Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA ygrad@hsph.harvard.edu.
authors.forename: Yonatan H
authors.initials: YH
authors.lastname: Grad
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors.forename: Ruchi
authors.initials: R
authors.lastname: Newman
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Zody
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yang
authors.affiliation: Department of Pediatrics, University of Tennessee School of Medicine, Memphis, Tennessee, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Murphy
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors.forename: James
authors.initials: J
authors.lastname: Qu
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Malboeuf
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.affiliation: Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Lipsitch
authors.affiliation: Department of Pediatrics, University of Tennessee School of Medicine, Memphis, Tennessee, USA Department of Microbiology, Immunology, and Molecular Biology, University of Tennessee School of Medicine, Memphis, Tennessee, USA Children's Foundation Research Institute, LeBonheur Children's Hospital, Memphis, Tennessee, USA.
authors.forename: John
authors.initials: J
authors.lastname: DeVincenzo
mesh_terms: D056704:Adaptive Immunity / Q000235:genetics*; D000595:Amino Acid Sequence; D014644:Genetic Variation / Q000235:genetics*; D016679:Genome, Viral; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016867:Immunocompromised Host / Q000235:genetics*; D008969:Molecular Sequence Data; D011446:Prospective Studies; D018357:Respiratory Syncytial Virus Infections / Q000235:genetics* / Q000276:immunology / Q000821:virology; D018113:Respiratory Syncytial Virus, Human / Q000235:genetics* / Q000302:isolation & purification; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D014764:Viral Proteins
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