Genetic Recombination between Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2, Two Distinct Human Lentiviruses

Abstract

Human immunodeficiency virus type 1 (HIV-1) and HIV-2 are genetically distinct viruses that each can cause AIDS. Approximately 1 million people are infected with both HIV-1 and HIV-2. Additionally, these two viruses use the same receptor and coreceptors and can therefore infect the same target cell populations. To explore potential genetic interactions, we first examined whether RNAs from HIV-1 and HIV-2 can be copackaged into the same virion. We used modified near-full-length viruses that each contained a green fluorescent protein gene (gfp) with a different inactivating mutation. Thus, a functional gfp could be reconstituted via recombination, which was used to detect the copackaging of HIV-1 and HIV-2 RNAs. The GFP-positive (GFP ؉ ) phenotype was detected in approximately 0.2% of the infection events, which was 35-fold lower than the intrasubtype HIV-1 rates. We isolated and characterized 54 GFP ؉ single-cell clones and determined that all of them contained proviruses with reconstituted gfp. We then mapped the general structures of the recombinant viruses and characterized the recombination junctions by DNA sequencing. We observed several different recombination patterns, including those that had crossovers only in gfp. The most common hybrid genomes had heterologous long terminal repeats. Although infrequent, crossovers in the viral sequences were also identified. Taken together, our study demonstrates that HIV-1 and HIV-2 can recombine, albeit at low frequencies. These observations indicate that multiple factors are likely to restrict the generation of viable hybrid HIV-1 and HIV-2 viruses. However, considering the large coinfected human population and the high viral load in patients, these rare events could provide the basis for the generation of novel human immunodeficiency viruses.

Determining the Frequency and Mechanisms of HIV-1 and HIV-2 RNA Copackaging by Single-Virion Analysis

“…We have previously measured recombination betwen HIV-1 and HIV-2 using two modified genomes, each carrying a mutated green fluorescent protein (gfp) gene; recombination between the two mutated genes could reconstitute a functional gfp gene, and its expression could be measured. We found that a very small percentage (ϳ0.5%) of infected cells had a GFP ϩ phenotype (25), which is much lower than that generated between two HIV-1 or two HIV-2 viruses (ϳ7%) (5,29). In all three studies, the gfp gene was used as a target sequence for reporting recombination; thus, regardless of the sequence diversity elsewhere in the viral genomes, the target regions between the mutations in the gfp genes contain identical sequences.…”

“…For example, despite sharing a low level of amino acid sequence identity, the Gag polyproteins from HIV-1 and HIV-2 can coassemble into the same particle and complement each other's functions to carry out infection (2). It has also been shown in a cell culture system that HIV-1 and HIV-2 can recombine and generate hybrid genomes, albeit at a rate far lower than that occurring between two HIV-1 or between two HIV-2 genomes (25). Retroviral recombination is the result of the reverse transcriptase (RT) switching between the two copackaged RNA templates during DNA synthesis.…”

The Remarkable Frequency of Human Immunodeficiency Virus Type 1 Genetic Recombination

“…For example, although naturally arising recombinants have been reported for HIV-2 (206, 315, 351), as have experimental recombinants between HIV-1 and HIV-2 (217), no natural HIV-1/HIV-2 recombinants have been reported (71,210) despite high rates of dual infection (327). Reasons for this may include limited cell coinfection and differences in RNA packaging (161,217,265). Additionally, the compartmentalization of virus strains to particular organs or other isolated sites can limit effective population sizes and thus the potential for recombination (7,171,223).…”

SHAPE analysis of the 5′ end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization

“…Therefore, it is not surprising that a number of recent cross-and copackaging studies have elucidated that the specificity of retroviral gRNA packaging can be manipulated by substituting dimerization and packaging sequences at the 5 ′ end of genome from genetically distinct retroviruses (Al Dhaheri et al 2009;Al Shamsi et al 2011). This has further been substantiated by the fact that heterodimers involving RNAs from two divergent retroviruses can also be packaged (Motomura et al 2008;for review, see Johnson and Telesnitsky 2010).…”