High Frequency of Genetic Recombination Is a Common Feature of Primate Lentivirus Replication

Abstract

Recent studies indicate that human immunodeficiency virus type 1 (HIV-1) recombines at exceedingly high rates, approximately 1 order of magnitude more frequently than simple gammaretroviruses such as murine leukemia virus and spleen necrosis virus. We hypothesize that this high frequency of genetic recombination is a common feature of primate lentiviruses. Alternatively, it is possible that HIV-1 is unique among primate lentiviruses in possessing high recombination rates. Among other primate lentiviruses, only the molecular mechanisms of HIV-2 replication have been extensively studied. There are reported differences between the replication mechanisms of HIV-1 and those of HIV-2, such as preferences for RNA packaging in cis and properties of reverse transcriptase and RNase H activities. These biological disparities could lead to differences in recombination rates between the two viruses. Currently, HIV-1 is the only primate lentivirus in which recombination rates have been measured. To test our hypothesis, we established recombination systems to measure the recombination rates of two other primate lentiviruses, HIV-2 and simian immunodeficiency virus from African green monkeys (SIVagm), in one round of viral replication. We determined that, for markers separated by 588, 288, and 90 bp, HIV-2 recombined at rates of 7.4%, 5.5%, and 2.4%, respectively, whereas SIVagm recombined at rates of 7.8%, 5.6%, and 2.7%, respectively. These high recombination rates are within the same range as the previously measured HIV-1 recombination rates. Taken together, our results indicate that HIV-1, HIV-2, and SIVagm all possess high recombination frequencies; hence, the high recombination potential is most likely a common feature of primate lentivirus replication.

The Remarkable Frequency of Human Immunodeficiency Virus Type 1 Genetic Recombination

“…For both HIV-1 and gammaretroviruses, reducing RNase H activity decreased template switching (37,234). These findings suggested that retroviruses with low RNase H activity, such as HIV-2 (132), would recombine less frequently than HIV-1, which possesses robust RNase H. However, subsequent studies demonstrated that rates of template switching are very similar for HIV-2 and HIV-1 (50,221).…”

“…The current consensus from experimental studies is that HIV-1 recombinogenic template switching occurs at the remarkable rate of roughly every 2 kb or possibly even more frequently under some physiological conditions (11,50,275). This section introduces the approaches that led to these conclusions and the properties of virus replication that are responsible.…”

“…It was thought that the performance of one recombination event predisposed a virus to performing additional switches or that only a subset of virions was prone to generating recombinant products due to flaws in viral nucleoprotein complex architecture (15,133,152). However, biases in gRNA packaging remove the need to evoke such models and suggest that recombination occurs at a similar high frequency for many if not all retroviruses (50,221,240,368). This can also explain differences between MLV and HIV-1 in minus strong-stop switching.…”

Identifying Recombination Hot Spots in the HIV-1 Genome

“…Studies to date have measured recombination rates in a number of elegant ways. The use of retroviral reporter systems, where correctly positioned recombination will recreate a functional foreign gene insert conferring antibiotic resistance or fluorescence (16)(17)(18), allows for the rapid screening of recombinants but does not allow the measurement of recombination on the natural HIV-1 sequence. A more direct method of detecting recombination is through the sequenc-ing of reverse transcription products derived from an authentic HIV-1 replication cycle.…”

Fifteen to Twenty Percent of HIV Substitution Mutations Are Associated with Recombination

“…Others have taken advantage of retroviral vector or reporter systems, in which the expressions of reporter genes (such as fluorescent proteins, cell surface markers, and/or antibiotic resistance genes) were used to select cells containing recombined viral genomes for recombination and mutation analyses (28)(29)(30)(31)(35)(36)(37)(38)(39). As coexpression of reporter gene products in a single cell is needed to identify recombination events, these systems generally use a low multiplicity of infection (MOI) to avoid dual infection introducing experimental bias (28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39). However, as these systems require expression of the gene products, natural mutation events or recombination events that lead to nonproductive expression of reporter genes will be unaccounted for.…”