title: Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination.
abstract: BACKGROUND
  HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system) and absence (in vitro reverse transcription and single cycle infection systems) of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D) were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population.
  
  
  RESULTS
  Increased sequence identity between viruses or RNA templates resulted in increased recombination frequencies, with the exception of the 115-A virus or RNA template. Analyses of the recombination breakpoints and mechanistic studies revealed that the presence of a recombination hotspot in the C3/V4 env region, unique to 115-A as donor RNA, could account for the higher recombination frequencies with the 115-A virus/template. Single-cycle infections supported proportionally less recombination than the in vitro reverse transcription assay but both systems still had significantly higher recombination frequencies than observed in the multiple-cycle virus replication system. In the multiple cycle assay, increased replicative fitness of one HIV-1 over the other in a dual infection dramatically decreased recombination frequencies.
  
  
  CONCLUSIONS
  Sequence variation at specific sites between HIV-1 isolates can introduce unique recombination hotspots, which increase recombination frequencies and skew the general observation that decreased HIV-1 sequence identity reduces recombination rates. These findings also suggest that the majority of intra- or intersubtype A/D HIV-1 recombinants, generated with each round of infection, are not replication-competent and do not survive in the multiple-cycle system. Ability of one HIV-1 isolate to outgrow the other leads to reduced co-infections, heterozygous virus production, and recombination frequencies.
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA. heather_baird@dhiusa.com
authors.forename: Heather A
authors.initials: HA
authors.lastname: Baird
authors.forename: Yong
authors.initials: Y
authors.lastname: Gao
authors.forename: Román
authors.initials: R
authors.lastname: Galetto
authors.forename: Matthew
authors.initials: M
authors.lastname: Lalonde
authors.forename: Reshma M
authors.initials: RM
authors.lastname: Anthony
authors.forename: Véronique
authors.initials: V
authors.lastname: Giacomoni
authors.forename: Measho
authors.initials: M
authors.lastname: Abreha
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Destefano
authors.forename: Matteo
authors.initials: M
authors.lastname: Negroni
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Arts
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D002874:Chromosome Mapping; D015752:Genes, env; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D006801:Humans; D012367:RNA, Viral / Q000737:chemistry; D011995:Recombination, Genetic; D014454:Uganda; D014779:Virus Replication
chemical_list: D012367:RNA, Viral