Human Immunodeficiency Virus Type 1 Genetic Recombination Is More Frequent Than That of Moloney Murine Leukemia Virus despite Similar Template Switching Rates

Abstract

Retroviral recombinants result from template switching between copackaged viral genomes. Here, marker reassortment between coexpressed vectors was measured during single replication cycles, and human immunodeficiency virus type 1 (HIV-1) recombination was observed six-to sevenfold more frequently than murine leukemia virus (MLV) recombination. Template switching was also assayed by using transduction-type vectors in which donor and acceptor template regions were joined covalently. In this situation, where RNA copackaging could not vary, MLV and HIV-1 template switching rates were indistinguishable. These findings argue that MLV's lower intermolecular recombination frequency does not reflect enzymological differences. Instead, these data suggest that recombination rates differ because coexpressed MLV RNAs are less accessible to the recombination machinery than are coexpressed HIV RNAs. This hypothesis provides a plausible explanation for why most gammaretrovirus recombinants, although relatively rare, display evidence of multiple nonselected crossovers. By implying that recombinogenic template switching occurs roughly four times on average during the synthesis of every MLV or HIV-1 DNA, these results suggest that virtually all products of retroviral replication are biochemical recombinants.

Dynamics of HIV-1 recombination in its natural target cells

“…We calculate nine RSTE per virus in primary CD4 ϩ T lymphocytes. The agreement between the sequence analysis, which provides RSTE frequency in individual viruses known a priori to be recombinants, and the flow-cytometric method, which yields an average RSTE frequency across the entire population, suggests that most or all viruses are undergoing recombination, consistent with two recent reports (13,22). If recombination were occurring within only a subset of viruses (23), then the set of viruses identified as recombinants by their GFP expression would display a greater than average number of RSTE, which is not the case.…”

“…have shown that HIV-1 is about one order of magnitude more recombinogenic than several other retroviruses, including Maloney murine leukemia virus and human T cell leukemia virus type 1 (HTLV-1), during infection of identical cell types. HIV-1 infection of macrophages results in recombination frequencies nearly two logs higher than reported for infection of murine leukemia virus and spleen necrosis virus in fibroblast cell lines (13,22). It is possible that HIV-1 may have evolved higher recombination rates to foster more rapid diversification and promote its survival.…”

“…Second, one-half of the RSTE within this region will begin on the CFP gene and end on YFP, thus removing the two critical residues and generating a modified GFP gene (which we designate ''GFP*'') sequence. Third, approximately one-half of all HIV-1 virions produced from coexpressing cells will be heterozygous, whereas the other half will be homozygous (13). Thus, 0.04 ϫ 0.5 ϫ 0.5 ϭ 0.01, or 1% of all RSTE within the HIV-1 genome, will produce GFP*.…”

Evidence of intratypic recombination in natural populations of hepatitis C virus

“…The recombination breakpoint for non-segmented positive-strand RNA viruses, such as polioviruses and other picornaviruses (Santti et al, 1999;Guillot et al, 2000;Kew et al, 2002), as well as members of the family Flaviviridae, are often located in the part of the genome encoding the non-structural proteins but sometimes in genes encoding structural proteins (CostaMattioli et al, 2003;Martin et al, 2002). Moreover, several possible recombination breakpoints have been identified in other RNA viruses, such as human immunodeficiency virus (HIV), and many more are being reported (Onafuwa et al, 2003;Vidal et al, 2003;Strimmer et al, 2003;Najera et al, 2002). The recombination point in our recombinant strain was situated in the NS5B region (see Figs 2 and 3).…”

The Structure of HIV-1 Genomic RNA in the gp120 Gene Determines a Recombination Hot Spot in Vivo

“…Several efforts have been made in this sense during the last decade, and various mechanisms have been proposed, based either on the infection of cells in culture (ex vivo systems) (7,8) or on the reconstitution of the process of reverse transcription with purified proteins and nucleic acids (in vitro systems) (9 -12). Some hard facts have been jointly established by these two approaches, including the enhancement of template switching observed by decreasing the rate of DNA synthesis (13,14) and the importance of a temporal coupling of RT-encoded polymerase and RNaseH activities (8,15).…”