Open Access Research

Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination

Heather A Baird12, Yong Gao1, Román Galetto3, Matthew Lalonde14, Reshma M Anthony5, Véronique Giacomoni3, Measho Abreha1, Jeffrey J Destefano5, Matteo Negroni3 and Eric J Arts12*

Author Affiliations

1 Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA

2 Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, USA

3 Unité des Regulation Enzymatique et Activités Cellulaires, Institut Pasteur, Paris, Cedex 15, 75724, France

4 Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA

5 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA

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Retrovirology 2006, 3:91  doi:10.1186/1742-4690-3-91

Published: 12 December 2006



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.


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.


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.