title: Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection.
abstract: Resistance following antiviral therapy is commonly observed in human influenza viruses. Although this evolutionary process is initiated within individual hosts, little is known about the pattern, dynamics, and drivers of antiviral resistance at this scale, including the role played by reassortment. In addition, the short duration of human influenza virus infections limits the available time window in which to examine intrahost evolution. Using single-molecule sequencing, we mapped, in detail, the mutational spectrum of an H3N2 influenza A virus population sampled from an immunocompromised patient who shed virus over a 21-month period. In this unique natural experiment, we were able to document the complex dynamics underlying the evolution of antiviral resistance. Individual resistance mutations appeared weeks before they became dominant, evolved independently on cocirculating lineages, led to a genome-wide reduction in genetic diversity through a selective sweep, and were placed into new combinations by reassortment. Notably, despite frequent reassortment, phylogenetic analysis also provided evidence for specific patterns of segment linkage, with a strong association between the hemagglutinin (HA)- and matrix (M)-encoding segments that matches that previously observed at the epidemiological scale. In sum, we were able to reveal, for the first time, the complex interaction between multiple evolutionary processes as they occur within an individual host.
  
  
  OBJECTIVE
  Understanding the evolutionary forces that shape the genetic diversity of influenza virus is crucial for predicting the emergence of drug-resistant strains but remains challenging because multiple processes occur concurrently. We characterized the evolution of antiviral resistance in a single persistent influenza virus infection, representing the first case in which reassortment and the complex patterns of drug resistance emergence and evolution have been determined within an individual host. Deep-sequence data from multiple time points revealed that the evolution of antiviral resistance reflects a combination of frequent mutation, natural selection, and a complex pattern of segment linkage and reassortment. In sum, these data show how immunocompromised hosts may help reveal the drivers of strain emergence.
authors: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
authors: Matthew B
authors: MB
authors: Rogers
authors: Timothy
authors: T
authors: Song
authors: Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors: Robert
authors: R
authors: Sebra
authors: Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Oncology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors: Benjamin D
authors: BD
authors: Greenbaum
authors: Department of Infectious Diseases and Microbiology, Laval University and CHU of Quebec Hospital, Quebec, Quebec, Canada.
authors: Marie-Eve
authors: ME
authors: Hamelin
authors: Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
authors: Adam
authors: A
authors: Fitch
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.
authors: Alan
authors: A
authors: Twaddle
authors: Lijia
authors: L
authors: Cui
authors: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
authors: Edward C
authors: EC
authors: Holmes
authors: Department of Infectious Diseases and Microbiology, Laval University and CHU of Quebec Hospital, Quebec, Quebec, Canada guy.boivin@crchul.ulaval.ca elodie.ghedin@nyu.edu.
authors: Guy
authors: G
authors: Boivin
authors: guy.boivin@crchul.ulaval.ca elodie.ghedin@nyu.edu.
authors: Elodie
authors: E
authors: Ghedin
mesh_terms: D000998:Antiviral Agents / Q000627:therapeutic use*; D024882:Drug Resistance, Viral; D019143:Evolution, Molecular; D006801:Humans; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000188:drug therapy* / Q000821:virology*; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D000998:Antiviral Agents; D012367:RNA, Viral