Email updates

Keep up to date with the latest news and content from Retrovirology and BioMed Central.

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

For all author emails, please log on.

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

Published: 12 December 2006

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.

Conclusion

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.