High rates of human immunodeficiency virus type 1 recombination: near-random segregation of markers one kilobase apart in one round of viral replication

Evidence for preferential copackaging of Moloney murine leukemia virus genomic RNAs transcribed in the same chromosomal site

Background

Retroviruses have a diploid genome and recombine at high frequency. Recombinant proviruses can be generated when two genetically different RNA genomes are packaged into the same retroviral particle. It was shown in several studies that recombinant proviruses could be generated in each round of HIV-1 replication, whereas the recombination rates of SNV and Mo-MuLV are 5 to 10-fold lower. The reason for these differences is not clear. One possibility is that these retroviruses may differ in their ability to copackage genomic RNAs produced at different chromosomal loci.

Results

To investigate whether there is a difference in the efficiency of heterodimer formation when two proviruses have the same or different chromosomal locations, we introduced two different Mo-MuLV-based retroviral vectors into the packaging cell line using either the cotransfection or sequential transfection procedure. The comparative study has shown that the frequency of recombination increased about four-fold when the cotransfection procedure was used. This difference was not associated with possible recombination of retroviral vectors during or after cotransfection and the ratios of retroviral virion RNAs were the same for two variants of transfection.

Conclusions

The results of this study indicate that a mechanism exists to enable the preferential copackaging of Mo-MuLV genomic RNA molecules that are transcribed on the same DNA template. The properties of Mo-MuLV genomic RNAs transport, processing or dimerization might be responsible for this preference. The data presented in this report can be useful when designing methods to study different aspects of replication and recombination of a diploid retroviral genome.

Viral error catastrophe by mutagenic nucleosides

Riboviruses and retroviruses have the highest rates of mutations of any known organism. Increasing the mutation rate of these viruses could exceed the error threshold for viability of a viral population within a host. Recent experiments with mutagenic nucleoside analogs validate this new approach to treating infection of RNA viruses. Lethal mutagenesis with HIV-infected cells in culture has been documented and has been postulated to be the mechanism for treatment of hepatitis C with ribavirin. We consider the viral dynamics involved in the formation of a quasispecies, the choice of mutagenic nucleoside analogs, and the studies that have demonstrated the feasibility of lethal mutagenesis.

Effects of unpaired nucleotides within HIV-1 genomic secondary structures on pausing and strand transfer

Reverse transcriptase-mediated RNA displacement synthesis is required for DNA polymerization through the base-paired stem portions of secondary structures present in retroviral genomes. These regions of RNA duplex often possess single unpaired nucleotides, or "bulges," that disrupt contiguous base pairing. By using well defined secondary structures from the human immunodeficiency virus, type 1 (HIV-1), genome, we demonstrate that removal of these bulges either by deletion or by introducing a complementary base on the opposing strand results in increased pausing at specific positions within the RNA duplex. We also show that the HIV-1 nucleocapsid protein can increase synthesis through the pause sites but not as efficiently as when a bulge residue is present. Finally, we demonstrate that removing a bulge increases the proportion of strand transfer events to an acceptor template that occur prior to complete replication of a donor template secondary structure. Together our data suggest a role for bulge nucleotides in enhancing synthesis through stable secondary structures and reducing strand transfer.

Nonrandom dimerization of murine leukemia virus genomic RNAs

Retroviral genomes consist of two unspliced RNAs linked noncovalently in a dimer. Although these two RNAs are generally identical, two different RNAs can be copackaged when virions are produced by coinfected cells. It has been assumed, but not tested, that copackaging results from random RNA associations in the cytoplasm to yield encapsidated RNA homodimers and heterodimers in Hardy-Weinberg proportions. Here, virion RNA homo- and heterodimerization were examined for Moloney murine leukemia virus (MLV) using nondenaturing Northern blotting and a novel RNA dimer capture assay. The results demonstrated that coexpressed MLV RNAs preferentially self-associated, even when RNAs were identical in known packaging and dimerization sequences or when they differed overall by less than 0.1%. In contrast, HIV-1 RNAs formed homo- and heterodimers in random proportions. We speculate that these species-specific differences in RNA dimer partner selection may at least partially explain the higher frequency of genetic recombination observed for human immunodeficiency virus type 1 than for MLV.

Analysis of near full-length genome sequences of HIV type 1 BF intersubtype recombinant viruses from Brazil reveals their independent origins and their lack of relationship to CRF12_BF

We analyze the recombinant structures and phylogenetic relationships of nine near full-length genome sequences of HIV-1 BF intersubtype recombinant viruses from Brazil, eight of them newly derived. These were obtained by PCR amplification from peripheral blood mononuclear cells (PBMCs) DNA or PBMCs culture supernantant RNA. The recombinants exhibited unique mosaic structures, except two viruses with a single near coincident breakpoint. Comparison with CRF12_BF revealed only two coincident breakpoints in two recombinants. Phylogenetic analyses failed to support a common ancestry of Brazilian recombinants or their relationship to CRF12_BF, which widely circulates in Argentina. Intersubtype breakpoint distribution along the genome was uneven, with the highest mean frequency in the polymerase domain of reverse transcriptase, and the lowest in env. These results indicate that HIV-1 BF recombinants from Brazil have independent origins and are unrelated to CRF12_BF, and that intersubtype breakpoints are frequent in pol segments analyzed for drug resistance detection.

Antiretroviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase increase template-switching frequency

Template-switching events during reverse transcription are necessary for completion of retroviral replication and recombination. Structural determinants of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) that influence its template-switching frequency are not known. To identify determinants of HIV-1 RT that affect the frequency of template switching, we developed an in vivo assay in which RT template-switching events during viral replication resulted in functional reconstitution of the green fluorescent protein gene. A survey of single amino acid substitutions near the polymerase active site or deoxynucleoside triphosphate-binding site of HIV-1 RT indicated that several substitutions increased the rate of RT template switching. Several mutations associated with resistance to antiviral nucleoside analogs (K65R, L74V, E89G, Q151N, and M184I) dramatically increased RT template-switching frequencies by two- to sixfold in a single replication cycle. In contrast, substitutions in the RNase H domain (H539N, D549N) decreased the frequency of RT template switching by twofold. Depletion of intracellular nucleotide pools by hydroxyurea treatment of cells used as targets for infection resulted in a 1.8-fold increase in the frequency of RT template switching. These results indicate that the dynamic steady state between polymerase and RNase H activities is an important determinant of HIV-1 RT template switching and establish that HIV-1 recombination occurs by the previously described dynamic copy choice mechanism. These results also indicate that mutations conferring resistance to antiviral drugs can increase the frequency of RT template switching and may influence the rate of retroviral recombination and viral evolution.

Mechanistic analysis of pause site-dependent and -independent recombinogenic strand transfer from structurally diverse regions of the HIV genome

Retroviral recombinants are generated by strand transfers occurring within internal regions of the viral genome and are a major source of genetic variability. Strand transfer has been linked to "pausing" occurring at secondary structures during synthesis by reverse transcriptase. Yet, weakly structured templates lacking strong pause sites also undergo efficient transfer. In this report, transfer crossover sites on high and low structured templates from the gag-pol frameshift region (GagPol) and the env (Env) regions, respectively, were determined by using a reconstituted in vitro strand transfer assay. The assay tested transfers occurring between a donor and acceptor template over a 150-nucleotide homologous region. The majority of crossovers were in a small 23-nucleotide region near a major pause site on GagPol, clearly indicating a pause-driven mechanism. In contrast, on Env, transfers were more dispersed clustering toward the end of the homologous region. Slowing down polymerization on Env by decreasing the dNTP concentration resulted in crossovers shifting toward the beginning of the homologous region. Removal of a small 38-nucleotide region at the 3'-end of the Env acceptor had a large effect on the level of strand transfer despite very few crossovers mapping to this region. This implicated this part of the acceptor in transfers occurring at downstream positions. For Env the results support a mechanism where the acceptor rapidly binds nascent DNA, then "zippers" downstream catching up with the donor-DNA hybrid and displacing the donor. Such a mechanism may be important to recombination in low structure regions of the HIV genome.

Second-site revertants of a simian immunodeficiency virus gp41 mutant defective in envelope glycoprotein incorporation

We previously characterized a series of small in-frame deletions within the C-terminal third of the simian immunodeficiency virus (SIV) gp41 cytoplasmic domain that significantly impair the incorporation of the envelope (Env) glycoprotein into particles and Env-mediated virus entry. Among these mutations, removal of Env residues 832-837 caused the most drastic defective phenotype. In the present study, we introduced the Delta832-837 deletion into the PBj1.9 molecular clone and investigated the effect of this env mutation on virus replication in the CEMx174 cell line. This in-frame deletion was found to severely compromise virus replication. Interestingly, long-term culture of the PBjEnvDelta832-837 mutant led to the emergence of two independent populations of revertant viruses that, while differing in the time point at which they appear, encode truncated gp41 cytoplasmic tails of similar lengths. The first emergent virus population contained a premature stop codon mutation at Env residue 778, whereas the late-appearing population harbored a stop codon mutation at Env residue 774, which results in the truncation of the gp41 cytoplasmic tail to 52 and 48 amino acids, respectively. Analysis of derivatives of PBjEnvDelta832-837 containing either the Tyr778stop or the Trp774stop mutations demonstrated that these second-site changes were sufficient to reverse the Env incorporation and infectivity defects imposed by the original Delta832-837 deletion, as well as to confer to the Env double mutants essentially wild-type replication kinetics. Our results thus provide further insight into the mechanisms underlying SIV adaptation to novel selective forces.

The population genetics and evolutionary epidemiology of RNA viruses

The authors discuss the main mechanisms of RNA virus evolution — mutation, recombination, natural selection, genetic drift and migration, and how these interact to shape the genetic structure of populations. The quasispecies model of RNA virus evolution is explained and the question of whether this model provides an accurate description of RNA virus evolution is discussed. Experiments that can be carried out to test the basic principles of evolutionary theory are briefly described. The authors review what such experiments have told us about virus evolution and, more widely, what these experiments have revealed in terms of general evolutionary principles. RNA viruses evolve quickly, so a detailed reconstruction of their epidemiological history can be undertaken. The authors show how epidemiological patterns of viruses result from their evolution at two different levels: within individual hosts (and vectors) and among hosts at the population level. Using several examples, including HIV and SARS, the authors describe how studying RNA virus evolution could be used to understand virus emergence. Finally, the important topics of the evolution of virulence and resistance to drugs are discussed.

RNA viruses are ubiquitous intracellular parasites that are responsible for many emerging diseases, including AIDS and SARS. Here, we discuss the principal mechanisms of RNA virus evolution and highlight areas where future research is required. The rapidity of sequence change in RNA viruses means that they are useful experimental models for the study of evolution in general and it enables us to watch them change in 'real time', and retrace the spread through populations with molecular phylogenies. An understanding of the mechanisms of RNA virus sequence change is also crucial to predicting important aspects of their emergence and long-term evolution.

Dynamics of HIV-1 recombination in its natural target cells

Genetic recombination is believed to assist HIV-1 diversification and escape from host immunity and antiviral therapies, yet this process remains largely unexamined within the natural target-cell populations. We developed a method for measuring HIV-1 recombination directly that employs reporter viruses bearing functional enhanced yellow fluorescent protein (YFP) and enhanced cyan fluorescent protein (CFP) genes in which recombination produces a modified GFP gene and GFP fluorescence in the infected cells. These reporter viruses allow simultaneous quantification of the dynamics of HIV-1 infection, coinfection, and recombination in cell culture and in animal models by flow-cytometric analysis. Multiround infection assays revealed that productive cellular coinfection was subject to little functional inhibition. As a result, generation of recombinants proceeded according to the square of the infection rate during HIV-1 replication in T lymphocytes and within human thymic grafts in severe combined immunodeficient (SCID)-hu (Thy/Liv) mice. These results suggest that increases in viral load may confer a compounding risk of virus escape by means of recombinational diversification. A single round of replication in T lymphocytes in culture generated an average of nine recombination events per virus, and infection of macrophages led to approximately 30 crossover events, making HIV-1 up to an order of magnitude more recombinogenic than recognized previously and demonstrating that the infected cell exerts a profound influence on the frequency of recombination.