Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Oct;80(19):9651-8.
doi: 10.1128/JVI.00936-06.

High frequency of genetic recombination is a common feature of primate lentivirus replication

Jianbo Chen  1 , Douglas Powell, Wei-Shau Hu
Affiliations

High frequency of genetic recombination is a common feature of primate lentivirus replication

Jianbo Chen et al. J Virol. 2006 Oct.

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.

PubMed Disclaimer

Figures

FIG. 1.
FIG. 1.
General structure of HIV-2 vectors used to measure recombination rates. All vectors share the same structure but differ in the marker genes carried. Asterisks indicate inactivating mutations in GFP. LTR, long terminal repeat.
FIG. 2.
FIG. 2.
Representative flow cytometry analyses of mock-infected and infected target cells. (A and B) Mock-infected Hut/CCR5 target cells stained with anti-HSA and anti-Thy-1 antibodies. (C and D) Hut/CCR5 target cells infected with virus harvested from a producer cell line harboring both HIV2-H0G and HIV2-T600G; cells were stained with anti-HSA and anti-Thy-1 antibodies. Expression levels of marker genes are indicated on the x and y axes.
FIG. 3.
FIG. 3.
General structure of SIVagm vectors used to measure recombination rates. All vectors share the same structure but differ in the marker genes carried. Asterisks indicate inactivating mutations in GFP. LTR, long terminal repeat.
FIG. 4.
FIG. 4.
Representative flow cytometry analyses of mock-infected and infected target cells. (A and B) Mock-infected Hut/CCR5 target cells stained with anti-HSA and anti-Thy-1 antibodies. (C and D) Hut/CCR5 target cells infected with virus harvested from a producer cell line harboring both Tan-H0G and Tan-T600G.
FIG. 5.
FIG. 5.
Comparison of HIV-2, SIVagm, and HIV-1 recombination rates. The previously described model of the relationship between HIV-1 recombination rate and marker distance is shown as a solid line, and its 95% confidence bands are shown as dashed lines. The 95% confidence band was computed by adding two estimated standard errors of estimate to predicted scores. The measured HIV-2 and SIVagm recombination rates at three marker distances (from Tables 1 and 2) are indicated by triangles and circles, respectively.
See this image and copyright information in PMC

References

    1. Anderson, J. A., E. H. Bowman, and W. S. Hu. 1998. Retroviral recombination rates do not increase linearly with marker distance and are limited by the size of the recombining subpopulation. J. Virol. 72:1195-1202. - PMC - PubMed
    1. Anderson, J. A., V. K. Pathak, and W. S. Hu. 2000. Effect of the murine leukemia virus extended packaging signal on the rates and locations of retroviral recombination. J. Virol. 74:6953-6963. - PMC - PubMed
    1. Bailes, E., F. Gao, F. Bibollet-Ruche, V. Courgnaud, M. Peeters, P. A. Marx, B. H. Hahn, and P. M. Sharp. 2003. Hybrid origin of SIV in chimpanzees. Science 300:1713. - PubMed
    1. Beer, B. E., E. Bailes, G. Dapolito, B. J. Campbell, R. M. Goeken, M. K. Axthelm, P. D. Markham, J. Bernard, D. Zagury, G. Franchini, P. M. Sharp, and V. M. Hirsch. 2000. Patterns of genomic sequence diversity among their simian immunodeficiency viruses suggest that L'Hoest monkeys (Cercopithecus lhoesti) are a natural lentivirus reservoir. J. Virol. 74:3892-3898. - PMC - PubMed
    1. Beer, B. E., E. Bailes, R. Goeken, G. Dapolito, C. Coulibaly, S. G. Norley, R. Kurth, J.-P. Gautier, A. Gautier-Hion, D. Vallet, P. M. Sharp, and V. M. Hirsch. 1999. Simian immunodeficiency virus (SIV) from sun-tailed monkeys (Cercopithecus solatus): evidence for host-dependent evolution of SIV within the C. lhoesti superspecies. J. Virol. 73:7734-7744. - PMC - PubMed

Publication types

LinkOut - more resources