title: Estimating the in-vivo HIV template switching and recombination rate.
abstract: BACKGROUND
  HIV recombination has been estimated in vitro using a variety of approaches, and shows a high rate of template switching per reverse transcription event. In-vivo studies of recombination generally measure the accumulation of recombinant strains over time, and thus do not directly estimate a comparable template switching rate.
  
  
  METHODS
  To examine whether the estimated in-vitro template switching rate is representative of the rate that occurs during HIV infection in vivo, we adopted a novel approach, analysing single genome sequences from early founder viruses to study the in-vivo template switching rate in the env region of HIV.
  
  
  RESULTS
  We estimated the in-vivo per cycle template switching rate to be between 0.5 and 1.5/1000 nt, or approximately 5-14 recombination events over the length of the HIV genome.
  
  
  CONCLUSIONS
  The in-vivo estimated template switching rate is close to the in-vitro estimated rate found in primary T lymphocytes but not macrophages, which is consistent with the majority of HIV infection occurring in T lymphocytes.
authors.affiliation: aComplex Systems in Biology Group, Centre for Vascular Research, University of New South Wales, KensingtonbInfection Analytics Program, Kirby Institute, University of New South WalescSchool of Public Health, Sydney University, Camperdown, New South WalesdSchool of Medicine, Faculty of Health, Deakin UniversityeCSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
authors.forename: Deborah
authors.initials: D
authors.lastname: Cromer
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Grimm
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Schlub
authors.forename: Johnson
authors.initials: J
authors.lastname: Mak
authors.forename: Miles P
authors.initials: MP
authors.lastname: Davenport
mesh_terms: D006678:HIV / Q000235:genetics* / Q000502:physiology*; D006801:Humans; D008264:Macrophages / Q000821:virology; D008962:Models, Theoretical; D011995:Recombination, Genetic; D048348:Reverse Transcription; D013601:T-Lymphocytes / Q000821:virology; D016662:Virus Integration