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Understanding the mechanisms of HIV-1 drug resistance is critical for developing more effective antiretroviral agents and therapies. Based on our previously described dynamic copy-choice mechanism for retroviral recombination and our observations that nucleoside reverse transcriptase inhibitors (NRTIs) increase the frequency of reverse transcriptase template switching, we propose that an equilibrium exists between ( i ) NRTI incorporation, NRTI excision, and resumption of DNA synthesis and ( ii ) degradation of the RNA template by RNase H activity, leading to dissociation of the template-primer and abrogation of HIV-1 replication. As predicted by this model, mutations in the RNase H domain that reduced the rate of RNA degradation conferred high-level resistance to 3′-azido-3′-deoxythymidine and 2,3-didehydro-2,3-dideoxythymidine by as much as 180- and 10-fold, respectively, by increasing the time available for excision of incorporated NRTIs from terminated primers. These results provide insights into the mechanism by which NRTIs inhibit HIV-1 replication and imply that mutations in RNase H could significantly contribute to drug resistance either alone or in combination with NRTI-resistance mutations in reverse transcriptase.

To investigate the extent to which drug resistance mutations are missed by standard genotyping methods, we analyzed the same plasma samples from 26 patients with suspected multidrug-resistant human immunodeficiency virus type 1 by using a newly developed single-genome sequencing technique and compared it to standard genotype analysis. Plasma samples were obtained from patients with prior exposure to at least two antiretroviral drug classes and who were on a failing antiretroviral regimen. Standard genotypes were obtained by reverse transcriptase (RT)-PCR and sequencing of the bulk PCR product. For single-genome sequencing, cDNA derived from plasma RNA was serially diluted to 1 copy per reaction, and a region encompassing p6, protease, and a portion of RT was amplified and sequenced. Sequences from 15 to 46 single viral genomes were obtained from each plasma sample. Drug resistance mutations identified by single-genome sequencing were not detected by standard genotype analysis in 24 of the 26 patients studied. Mutations present in less than 10% of single genomes were almost never detected in standard genotypes (1 of 86). Similarly, mutations present in 10 to 35% of single genomes were detected only 25% of the time in standard genotypes. For example, in one patient, 10 mutations identified by single-genome sequencing and conferring resistance to protease inhibitors (PIs), nucleoside analog reverse transcriptase inhibitors, and nonnucleoside reverse transcriptase inhibitors (NNRTIs) were not detected by standard genotyping methods. Each of these mutations was present in 5 to 20% of the 20 genomes analyzed; 15% of the genomes in this sample contained linked PI mutations, none of which were present in the standard genotype. In another patient sample, 33% of genomes contained five linked NNRTI resistance mutations, none of which were detected by standard genotype analysis. These findings illustrate the inadequacy of the standard genotype for detecting low-frequency drug resistance mutations. In addition to having greater sensitivity, single-genome sequencing identifies linked mutations that confer high-level drug resistance. Such linkage cannot be detected by standard genotype analysis.

Cells infected with two related retroviruses can generate heterozygous virions, which are the precursors of recombinant proviruses. Although many studies have focused on the frequencies and mechanisms of retroviral recombination, little is known about the dynamics of double infection. To examine this issue, viruses generated from two HIV-1 vectors containing different markers were mixed together, and were used to infect target cells. The numbers of cells expressing none, one, or both markers were measured and were used to calculate whether double infection occurred at frequencies expected from random infection events. We found that double infection occurred significantly more frequently than predicted from random distribution; increased rates of double infection were observed in both a T cell line and primary activated CD4 + T cells. In addition to direct virus infection, we also examined the nature of cell-mediated HIV-1 double infection. Increased double infection was observed in all experiments regardless of whether a cell line or primary human dendritic cells were used for capture and transmission of HIV-1. Therefore, our results indicate that HIV-1 double infection occurs more frequently than it would at random in both direct and cell-mediated HIV-1 infections. To our knowledge, this is the first direct evidence of nonrandom double infection in HIV-1. Frequent double HIV-1 infections in infected individuals would allow the generation of recombinant viruses that could then affect their pathogenesis and evolution.

Alpharetroviruses provide a useful system for the study of the molecular mechanisms of host range and receptor interaction. These viruses can be divided into subgroups based on diverse receptor usage due to variability within the two host range determining regions, hr1 and hr2, in their envelope glycoprotein SU (gp85). In previous work, our laboratory described selection from a subgroup B avian sarcoma-leukosis virus of an extended-host-range variant (LT/SI) with two adjacent amino acid substitutions in hr1. This virus retains its ability to use the subgroup BD receptor but can also infect QT6/BD cells, which bear a related subgroup E receptor (R. A. Taplitz and J. M. Coffin, J. Virol 71:7814-7819, 1997). Here, we report further analysis of this unusual variant. First, one (L154S) of the two substitutions is sufficient for host range extension, while the other (T155I) does not alter host range. Second, these mutations extend host range to non-avian cell types, including human, dog, cat, mouse, rat, and hamster. Third, interference experiments imply that the mutants interact efficiently with the subgroup BD receptor and possibly the related subgroup E receptor, but they have another means of entry that is not dependent on these interactions. Fourth, binding studies indicate that the mutant SU proteins retain the ability to interact as monomers with subgroup BD and BDE receptors but only bind the subgroup E receptor in the context of an Env trimer. Further, the mutant SU proteins bind well to chicken cells but do not bind any better than wild-type subgroup B to QT6 or human cells, even though the corresponding viruses are capable of infecting these cells.

SUMMARYWe present here a self-contained analytic review of the role of stochastic factors acting on a virus population. We develop a simple one-locus, two-allele model of a haploid population of constant size including the factors of random drift, purifying selection, and random mutation. We consider different virological experiments: accumulation and reversion of deleterious mutations, competition between mutant and wild-type viruses, gene fixation, mutation frequencies at the steady state, divergence of two populations split from one population, and genetic turnover within a single population. In the first part of the review, we present all principal results in qualitative terms and illustrate them with examples obtained by computer simulation. In the second part, we derive the results formally from a diffusion equation of the Wright-Fisher type and boundary conditions, all derived from the first principles for the virus population model. We show that the leading factors and observable behavior of evolution differ significantly in three broad intervals of population size, N. The “neutral limit” is reached when N is smaller than the inverse selection coefficient. When N is larger than the inverse mutation rate per base, selection dominates and evolution is “almost” deterministic. If the selection coefficient is much larger than the mutation rate, there exists a broad interval of population sizes, in which weakly diverse populations are almost neutral while highly diverse populations are controlled by selection pressure. We discuss in detail the application of our results to human immunodeficiency virus population in vivo, sampling effects, and limitations of the model.

Although retroviruses can integrate their DNA into a large number of sites in the host genome, factors controlling the specificity of integration remain controversial and poorly understood. To assess the effects of transcriptional activity on integration in vivo, we created quail cell clones containing a construct with a minigene cassette, whose expression is controlled by the papilloma virus E2 protein. From these clones we derived transcriptionally active subclones expressing the wild-type E2 protein and transcriptionally silent subclones expressing a mutant E2 protein that binds its target DNA but is unable to activate transcription. By infecting both clones and subclones with avian leukosis virus and using a PCR-based assay to determine viral DNA integration patterns, we were able to assess the effects of both protein binding and transcriptional activity on retroviral DNA integration. Contrary to the hypothesis that transcriptional activity enhances integration, we found an overall decrease in integration into our gene cassette in subclones expressing the wild-type E2 protein. We also found a decrease in integration into our gene cassette in subclones expressing the mutant E2 protein, but only into the protein binding region. Based on these findings, we propose that transcriptionally active DNA is not a preferred target for retroviral integration and that transcriptional activity may in fact be correlated with a decrease in integration.

T CELLS that recognize self antigen are clonally deleted in the thymus—a maturation process that occurs in the context of histo-compatibility molecules and the T-cell receptor. The minor lymphocyte stimulation antigens (Mis) effect these deletions through interactions with the Vβ portion of the T-cell receptor, thus mimicking bacterial 'superantigens'. Intrigued by the fact that each known Mls gene maps to the same chromosomal region as an endogenous mouse mammary tumour virus (Mtv), we re-evaluated the linkage relationships between the two gene families. Here we report perfect concordance in inbred and recombinant inbred mice between the presence of four Mtv proviruses with the expression of Mls gene products. These data suggest a general model in which mammary tumour virus gene products themselves are the ligands that shape a considerable portion of the immuno-logical repertoire of common laboratory mice.

The 3′ untranslated region (3′ UTR) between the 3′ end of env and the long terminal repeat is well conserved among avian retroviruses and is essential for efficient replication. Deletion of the dr1 element within the 3′ UTR has been reported to have various effects, including reduced levels of unspliced RNA in the cytoplasm, decreased stability of unspliced RNA, decreased particle production, and decreased genomic RNA packaging. To probe the role of specific sequences within dr1 in virus replication, site-directed mutagenesis was utilized to perturb parts of the predicted secondary structure of dr1. Seven of thirteen mutations had no significant effect; the others resulted in an approximately 10- to 20-fold reduction in replication. These mutants were further characterized and found to impair cytoplasmic accumulation of unspliced RNA only slightly. Furthermore, no decreases were observed in the stability of the unspliced RNA or in the production of virus particles. Genomic RNA packaging, however, was reduced by about 10-fold. Similar amounts of particles were produced by cells containing the mutant and wild-type DNA, and all particles contained similar levels of reverse transcriptase activity. The results suggest that the region of the dr1 disrupted by the mutations plays a role in genomic RNA packaging, although that packaging may not be the only role for dr1.

Publisher Summary Eradication of HIV from infected individuals and development of more effective therapeutic methods for its control remain a high priority of HIV research. Elucidating the dominant biological mechanisms responsible for persistence and stability of the HIV infection could greatly assist with these goals. This chapter reviews the current understanding of the dynamics of HIV and its host cells in infected individuals. To approach the problem of cell dynamics in HIV infection, the chapter analyzes a score of experimental features in a typical patient, both in the presence and in the absence of drug therapy, and use these facts as tests for a panel of mathematical models. The chapter has restricted the search to models that do not postulate that HIV impairs the homeostatic replenishment mechanism of T-cells, and models that do not include interaction of HIV-specific effector cells with uninfected permissive cells, or the interaction of infected cells with each other.

The primate APOBEC3 gene locus encodes a family of proteins (APOBEC3A-H) with various antiviral and anti-retroelement activities. Here, we trace the evolution of APOBEC3H activity in hominoids to identify a human-specific loss of APOBEC3H antiviral activity. Reconstruction of the predicted ancestral human APOBEC3H protein shows that human ancestors encoded a stable form of this protein with potent antiviral activity. Subsequently, the antiviral activity of APOBEC3H was lost via two polymorphisms that are each independently sufficient to destabilize the protein. Nonetheless, an APOBEC3H allele that encodes a stably expressed protein is still maintained at high frequency, primarily in African populations. This stable APOBEC3H protein has potent activity against retroviruses and retrotransposons, including HIV and LINE-1 elements. The surprising finding that APOBEC3H antiviral activity has been lost in the majority of humans may have important consequences for our susceptibility to retroviral infections as well as ongoing retroelement proliferation in the human genome.

Recent research advances have afforded substantially improved understanding of the biology of HIV infection and the pathogenesis of AIDS. With the advent of sensitive tools for monitoring HIV replication in infected persons, the risk for disease progression and death can be assessed accurately and the efficacy of anti-HIV therapies can be determined directly. Furthermore, when used appropriately, combinations of newly available, potent antiviral therapies can effect prolonged suppression of detectable levels of HIV replication and circumvent the inherent tendency of HIV to generate drug-resistant viral variants. However, as antiretroviral therapy for HIV infection has become increasingly effective, it has also become increasingly complex. Familiarity with recent research advances is needed to ensure that newly available therapies are used in ways that most effectively improve the health and prolong the lives of HIV-infected persons. To enable practitioners and HIV-infected persons to best use rapidly accumulating new information about HIV disease pathogenesis and treatment, the Office of AIDS Research of the National Institutes of Health (NIH) sponsored the NIH Panel To Define Principles of Therapy of HIV Infection. This Panel was asked to define essential scientific principles that should be used to guide the most effective use of antiretroviral therapies and viral load testing in clinical practice. On the basis of detailed consideration of the most current data, the Panel delineated 11 principles that address issues of fundamental importance for the treatment of HIV infection. These principles provide the scientific basis for the specific treatment recommendations made by the Panel on Clinical Practices for the Treatment of HIV Infection sponsored by the Department of Health and Human Services and the Henry J. Kaiser Family Foundation. The reports of both of these panels are provided in this supplement. Together, they summarize new data and provide both the scientific basis and specific guidelines for the treatment of HIV-infected persons. This information will be of interest to health care providers, HIV-infected persons, HIV and AIDS educators, public health educators, public health authorities, and all organizations that fund medical care of HIV-infected persons.

Expression of mouse mammary tumor virus (MMTV)-encoded superantigens in B lymphocytes is required for viral transmission and pathogenesis. The mechanism of superantigen expression from the viral sag gene in B cells is largely unknown, due to problems with detection and quantification of these low-abundance proteins. We have established a sensitive superantigen-luciferase reporter assay to study the expression and regulation of the MMTV sag gene in B-cell lymphomas. The regulatory elements for retroviral gene expression are generally located in the 5′ long terminal repeat (LTR) of the provirus. However, we found that neither promoters nor enhancers in the MMTV 5′ LTR play a significant role in superantigen expression in these cells. Instead, the essential regulatory regions are located in the pol and env genes of MMTV. We report here that maximal sag expression in B-cell lines depends on an enhancer within the viral pol gene which can be localized to a minimal 183-bp region. Regulation of sag gene expression differs between B-cell lymphomas and pro-B cells, where an enhancer within the viral LTRs is involved. Thus, MMTV sag expression during B-cell development is achieved through the use of two separate enhancer elements.

Intracisternal-A-particle-related envelope-encoding (IAPE) proviral elements in the mouse genome encode and express an envelope-like protein that may allow transmission of IAPEs as infectious agents. To test IAPE mobility and potential transmission in mice, we have analyzed the distribution of IAPE elements in the genomes of Mus spretus and Mus musculus inbred strains and wild-caught animals. Potential full-length (IAPE-A) proviral elements are present as repetitive copies in DNA from male but not female animals of M. musculus inbred strains and Mus musculus castaneus. Analysis of IAPE-cellular junction fragments indicates that fixation of most IAPEs in the germ line occurred in M. musculus and M. spretus after speciation but before M. musculus inbred strains were derived.

The genetic relationships between woodland and barren ground caribou herds are being investigated using both mitochondrial and nuclear D N A . D N A sequence variation i n the most variable region (the D l o o p region) o f mitochondrial D N A indicate the woodland caribou from Newfoundland, Ontario, Alberta, and Brit ish Co lumbia are closely related and form a monophyletic clade although introgression o f barren ground mitochondrial genotypes occur i n some herds. In addition, micro-satellites, w h i c h are highly variable nuclear loc i used for D N A finger printing, are being developed w h i c h can distinguish individuals w i t h i n and between herds.

EL/Suz (EL) mice experience recurrent seizures that are similar to common partial complex epilepsy in humans. In the mice, seizures occur naturally at 90–100 days of age, but can be induced in younger mice and analyzed as a semi-quantitative trait after gentle rhythmic stimulation. A previous genetic mapping study of EL backcrosses to the strains ABP/LeJ or DBA/2J showed two quantitative trait loci (QTL) with large effects on seizure frequency (El1, Chr 9; El2, Chr 2) and implied the existence of other QTL with lesser effects. To further the understanding of EL-derived seizure alleles, we examined intercross progeny of EL and the strains ABP/LeJ and DDY/Jcl, and also a backcross of (EL x DDY)F1 hybrids to DDY. A new large-effect seizure frequency QTL was found (El5, Chr 14), a more minor QTL confirmed (El3, Chr 10), and two additional QTL proposed (El4, Chr 9; El6, Chr 11). The serotonin receptor gene, Htr2a, maps near and is a candidate for El5, and linkages of other serotonin receptor genes to seizure frequency QTL are noted. In addition, a strong gender effect was revealed, and epistasis was found between Chr 9 and Chr 14 markers. Despite this progress, however, our results revealed a more complex determinism of epilepsy in EL mice than previously described. In particular, no single El locus or pair was essential for frequent seizures, as QTL with large effects, such as El5, El2, and El1, were highly dependent on genetic context. Our studies highlight the importance of gene interaction in some complex mammalian traits defined by natural variation.

The mechanisms regulating expression of mouse mammary tumor virus (MMTV)-encoded superantigens from the viral sag gene are largely unknown, due to problems with detection and quantification of these low-abundance proteins. To study the expression and regulation of the MMTV sag gene, we have developed a sensitive and quantitative reporter gene assay based on a recombinant superantigen-human placental alkaline phosphatase fusion protein. High sag-reporter expression in Ba/F3, an early B-lymphoid cell line, depends on enhancers in either of the viral long terminal repeats (LTRs) and is largely independent of promoters in the 5' LTR. The same enhancer region is also required for general expression of MMTV genes from the 5' LTR. The enhancer was mapped to a 548-bp fragment of the MMTV LTR lying within sag and shown to be sufficient to stimulate expression from a heterologous simian virus 40 promoter. No enhancer activity of the MMTV LTR was observed in XC sarcoma cells, which are permissive for MMTV. Our results demonstrate a major role for this enhancer in MMTV gene expression in early B-lymphoid cells.

We describe the cloning and sequence analysis of the region surrounding the gene for the alpha subunit of RNA polymerase from Chlamydia trachomatis. This region contains genes for proteins in the order SecY, S13, S11, alpha, and L17, which are equivalent to Escherichia coli and Bacillus subtilis r proteins. The incorporation of chlamydial alpha subunit protein into the E. coli RNA polymerase holoenzyme rather than its truncated variant lacking the amino terminus suggests the existence of structural conservation among alpha subunits from distantly related genera.

Several recent reports indicate that the long, clinically latent phase that characterizes human immunodeficiency virus (HIV) infection of humans is not a period of viral inactivity, but an active process in which cells are being infected and dying at a high rate and in large numbers. These results lead to a simple steady-state model in which infection, cell death, and cell replacement are in balance, and imply that the unique feature of HIV is the extraordinarily large number of replication cycles that occur during infection of a single individual. This turnover drives both the pathogenic process and (even more than mutation rate) the development of genetic variation. This variation includes the inevitable and, in principle, predictable accumulation of mutations such as those conferring resistance to antiviral drugs whose presence before therapy must be considered in the design of therapeutic strategies.

We characterized endogenous proviruses in C57BL/6J, DBA/2J, and C3H/HeJ mouse strains with oligonucleotide probes derived from long terminal repeat (LTR) sequences of three classes of nonecotropic murine leukemia virus. The segregation of proviral-host DNA junction fragments was followed in BXH and BXD recombinant inbred (RI) strain sets, and most fragments mapped readily to defined chromosomal regions. Most of the LTR fragments appear to correspond to proviruses mapped previously with oligonucleotide env region probes of the same viral class. At least 22 elements represent new proviral loci, no more than half of which may be solo LTRs, and an additional six may correspond to proviruses identified previously with less specific hybridization probes. Together with proviruses identified previously with env probes, the LTR probe-reactive elements represent the majority of endogenous murine leukemia proviruses in the mouse genome.

Xenotropic MLV-related retrovirus (XMRV) was first reported about 5 years ago in a few cases of prostate cancer, but did not attract much attention until its reported association with a large fraction of chronic fatigue syndrome cases about 2 years ago. The publication of the XMRV-CFS connection created a ripple of excitement and interest in the scientific, medical, and patient communities reminiscent of the reports of the association of another retrovirus—HIV-with AIDS some 25 years previously. Although I was not directly involved in either discovery at the time, I was a very interested observer who had been working with various retroviruses and who subsequently became involved in both HIV and XMRV research, and I will offer some observations on the parallels and differences between the two. It is noteworthy, that, within 2 years of the first report, in 1983, of the virus we now call HIV, the key findings were widely replicated by virologists using a variety of different assays. By contrast, most of the results of the XMRV paper - isolation of infectious virus from patients, frequent detection of virus in plasma and PBMCs by PCR, detection of antiviral antibodies - remain to be replicated outside of the laboratories that authored the original report despite considerable effort worldwide. HIV is now known as the cause of a global pandemic responsible for large numbers of deaths annually and considerable hardship and economic loss. By contrast, XMRV is considered by most virologists to be the consequence of a collection of artifacts originating from endogenous murine leukemia viruses prevalent in laboratory and wild mice. In this talk, I will discuss our recent work that uncovered how these associations arose and how even experienced retrovirologists were misled by the initial reports. There are several related, but distinct, issues that need to be considered. First, various mouse (Mus musculus) subspecies carry over a hundred different endogenous proviruses closely (>90%) related to XMRV in their DNA. Second, mice are extremely widespread, as is their DNA, which can be found sporadically on laboratory surfaces, as well as contaminants of common reagents and materials. Sensitive PCR assays can detect "XMRV" related sequences in DNA from tiny fractions of one cell. To detect such contamination, we developed a more sensitive assay based on mouse IAP sequences present in thousands of copies per cell. Third, although only a few of the endogenous MLV proviruses encode infectious virus, it has been known since the 1970s that some of them can give rise to virus that can infect human tumor lines when passaged through nude mice. Indeed, A virus identical to XMRV is produced by the 22RV1 prostate cancer line that was derived in just this way In initial reports, however, XMRV did not appear to be sufficiently similar to known proviruses to have been derived this way. However, we have recently shown that this is exactly how it did arise, but not from infection of the precursor CWR22 xenograft with a single virus, but rather with a recombinant between the progeny of two previously undescribed proviruses found in the nude mice used for passage. Since the predicted recombinant is ancestral to all XMRV isolates, and cannot have arisen more than once, it must have found its way into many laboratories as the 22Rv1 cell line was distributed worldwide and, by means that remain to be worked out, into clinical samples from CFS patients.

The Blood XMRV Scientific Research Working Group was formed to facilitate collaborative studies into the impact of XMRV in blood donors. Studies will evaluate XMRV detection assays in terms of sensitivity, specificity and reproducibility; assess performance on specimens represented in existing blood donor repositories, and determine the prevalence of XMRV in donors. Phase I utilized analytical performance panels spiked with XMRV infected cells or virus. These panels were tested in a blinded fashion using XMRV nucleic acid testing (NAT) assays developed by six participating laboratories, with all laboratories determined to have sensitive NAT assays. Phase II represented pilot studies to compare XMRV detection using PBMCs, WB and plasma derived from individuals identified as XMRV viremic and antibody positive in previous studies. An unblinded pilot study resulted in two laboratories detecting MLV-like sequences in the plasma, but not PBMCs or WB, from all four subjects. A third laboratory detected no viral sequences. A blinded pilot study using the same four subjects and two validated negatives was less conclusive, with 3/4 laboratories detecting no viral sequences with any of the samples. A FACS-based serological assay detected antibodies in 3/4 XMRV-positive individuals, but also in 1/2 negatives. Seroreactivity to XMRV was not observed in plasma samples by Western blot. Phase III involves further evaluation of the clinical sensitivity and specificity of candidate assays by using a blinded panel of 35 pedigreed positives, together with negatives and controls. Results are expected soon. Phase IV will test a blinded panel of 300 blood donor samples.

Background Human immunodeficiency virus (HIV) infection that persists despite antiretroviral therapy (ART) is a daunting problem. Given the limited evidence that resting CD4+ T cell infection (RCI) is affected by the histone deacetylase (HDAC) inhibitor valproic acid (VPA), we measured the stability of RCI and residual viremia in patients who added VPA with or without raltegravir (RAL), or enfuvirtide (ENF) with or without VPA, to standard ART. Methods Patients with plasma HIV RNA50%) was seen in six volunteers after the addition of RAL and VPA. In 4 of the 6 patients this lack of effect might be attributed to intermittent viremia, low VPA levels, or intermittent study therapy adherence. Overall, there was no effect of the addition of RAL or ENF on low-level viremia measured by SCA. Conclusions The prospective addition of VPA and RAL, VPA and ENF, or ENF failed to progressively reduce the frequency of RCI, or ablate intermittent and low-level viremia. New approaches such as more potent HDAC inhibition, alone or in combination with intensified ART or other agents that may disrupt proviral latency must be pursued.

Background The contribution of low frequency drug-resistant HIV-1 variants to failure of antiretroviral therapy is not well-defined in treatment-experienced patients.

The murine Mls-1 antigen is the prototype of endogenous superantigens, molecules whose activities lead to deletion of T cells expressing certain T-cell receptor V beta genes from the mature repertoire. However, Mls-1 also stimulates T cells expressing these particular V beta genes (V beta 6, V beta 7, V beta 8.1, and V beta 9) in vitro, making it one of the strongest known T-cell activators. We have recently reported that the Mls-1 gene is closely linked to the endogenous mammary tumor virus Mtv-7. We now demonstrate that Mls-1 is encoded by the open reading frame in the U3 region of the long terminal repeat of Mtv-7. However, control of expression of this molecule seems complex, depending on the promoter used for the transfection experiments. The sequence of the Mtv-7 open reading frame differs from all other known mammary tumor virus open reading frame sequences in the 3' end, suggesting that the T-cell receptor V beta specificity is conferred by the C terminus of the molecule. The predicted structure of the protein encoded by the open reading frame is consistent with a type II transmembrane molecule where the C terminus is extracellular.

Retroviruses can capture cellular sequences and express them as oncogenes. Capture has been proposed to be a consequence of the inefficiency of polyadenylation of the viral genome that allows the packaging of cellular sequences flanking the integrated provirus in virions; after transfer into virions, these sequences could be incorporated into the viral genome by illegitimate recombination during reverse transcription. As a test for this hypothesis, a tissue culture system was developed that mimics the transduction process and allows the analysis and quantitation of capture events in a single step. In this model, transduction of sequences adjacent to a provirus depends on the formation of readthrough transcripts and their transmission in virions and leads to various recombinant structures whose formation is independent of sequence similarity at the crossover site. Thus, all events in the transduction process can be attributed to the action of reverse transcriptase on readthrough transcripts without involving deletions of cellular DNA.

The retroviruses encompass a large family of infectious agents (Retroviridae) unified by a common virion structure and mode of replication. Retroviruses have been isolated from most vertebrate species in which they have been sought, and have been found to display a remarkable diversity in their association with the host. Table I gives a list of some of the more commonly encountered viruses. At the one end of the diversity, infections with some retroviruses can lead to uniformly fatal conditions, such as AIDS, a variety of malignancies, neurologic diseases, and other clinical conditions. At the other end, some retroviruses induce only a benign viremia with no outward adverse effects, and can even become established as DNA in the germ line and passed as “endogenous” viruses from generation to generation. Indeed, the line between endogenous viruses and the retrotransposable elements found in large numbers in the genome of all eukaryotes is very fine (Chapters 1 and 4). This chapter will be concerned with a discussion of general properties of the retroviruses, the structure of their virions, and their classification. Its scope will be limited to those elements which are demonstrably viruses.

Retroviruses are one of the most widespread and probably the most biologically diverse group of infectious agents of vertebrates. Virtually all mammals—as well as some birds, reptiles, and fish—have yielded infectious retroviruses when examined sufficiently closely. Within a species, the viruses isolated can display considerable diversity of biological properties. For example, within the group of closely related murine leukemia viruses are found agents which differ in receptors used for infection; in mode of transmission for genetic (as endogenous germline proviruses) to horizontal and vertical (via milk or infection in utero); in pathogenicity from benign to highly virulent; and in disease spectrum from a variety of malignancies of varying latency to immunodeficiencies, anemias, neurological diseases, and others.

As an approach to evaluating the contribution of classes of endogenous viral sequences to leukemogenesis, a genomic library was prepared from the highly tumorigenic AKR SL12.3 cell line and screened for env-containing proviruses. An extensive battery of virus-derived probes and specific oligonucleotide probes were used to segregate 83 positive clones into related groups. The nonecotropic endogenous retroviruses were identified as members of the polytropic, modified polytropic, or xenotropic groups. At least three unique xenotropic proviruses were detected that differed from the published xenotropic sequence within a variable region of the 5' portion of env. Changes among the xenotropic proviruses included relative insertions and/or deletions that maintain an open reading frame and hence the potential to encode viable envelope gene products. Several recombinant viruses were also detected. Recombination was not random and primarily involved the formation of mink cell focus-inducing class I retroviruses via recombination between polytropic elements and ecotropic virus. One other recombinant was detected which contained ecotropic virus sequences in the 5' region encoding p15 of an otherwise xenotropic provirus. An interesting observation was the finding that certain clones contained more than one provirus within the average 20-kb cloned insert. This would not be expected if integration were totally random. The de novo recombinant proviruses identified here provide a series of potential candidates to be evaluated for their contribution to the tumorigencity of the SL12.3 cell line.

The neurological mutant mouse strain E1 is a model for complex partial seizures in humans. The inheritance of epileptic seizures with seven conventional chromosomal markers and over 60 endogenous proviral markers was studied by means of back-crosses of E1 with two seizure-resistant strains, DBA/2J and ABP/LeJ. The major gene responsible for this epileptic phenotype (El-1) was localized to a region distal with respect to the centromere on chromosome 9. At least one other gene, El-2, linked to proviral markers on chromosome 2, also influences the seizure phenotype. In addition, a potential modifier of seizures was detected in the DBA/2J background. The location of El-1 on distal chromosome 9 may allow identification of an epilepsy candidate gene in humans on the basis of conserved synteny with human chromosome 3.

The spontaneous leukemias of AKR mice are caused by mink cell focus-forming (MCF) viruses. These viruses are generated by recombination between several endogenous murine retroviruses. The virological events leading to the generation of the leukemogenic agent were investigated by using an oligonucleotide specific for the U3 region of the leukemogenic virus and env-reactive oligonucleotide probes specific for the different classes of endogenous murine leukemia virus. It was shown that (i) the leukemogenic MCF virus is formed by recombination between at least three different endogenous sequences; (ii) the U3 donor for the leukemogenic virus is the inducible xenotropic virus Bxv-1; (iii) all spontaneous tumors contain viruses with duplicated enhancer regions in their long terminal repeats; (iv) enhancer duplication is a somatic event, since Bxv-1 contains only one copy; (v) the first recombinant virus detectable in mass populations of thymocytes by Southern hybridization analysis contains all structural features of the ultimate leukemogenic virus; and (vi) the multiple novel viruses in a given tumor represent progeny of the same unique recombination events. On the basis of these results, an analysis of the virological events leading to AKR thymomas is presented.

An in vitro integration system derived from avian leukosis virus-infected cells supports both intra- and intermolecular integration of the viral DNA. In the absence of polyethylene glycol, intramolecular integration of viral DNA molecules into themselves (autointegration) was preferred. In the presence of polyethylene glycol, integration into an exogenously supplied DNA target was greatly promoted. Analysis of integration intermediates revealed that the strand transfer mechanisms of both reactions were identical to those of retroviruses and some transposons: each 3' end of the donor molecule is joined to a 5' end of the cleaved target DNA. The immediate integration precursor appears to be linear viral DNA with the 3' ends shortened by 2 nucleotides. Finally, in the avian system, most cytoplasmic viral DNA appears to be incomplete and further DNA synthesis is required for integration in vitro.

We have developed a cell-free system for an avian retrovirus that promotes autointegration, one-long-terminal-repeat (LTR) circle formation, and correct integration into exogenous target DNA. In this system, autointegration and one-LTR circle formation occurred far more frequently than integration into exogenous target DNA. Autointegration had the same characteristics of normal integration into target DNA except in its selection of target. Highly efficient autointegration as well as one-LTR circle formation in vitro suggest that there may be a mechanism to prevent these processes in vivo.

Transgenic mice carrying an immunoglobulin μ heavy chain transgene exhibit isotype switching of the transgene. We have now characterized the mechanism of transgene switching in these mice. The site of μ transgene insertion in one transgenic line has been localized to chromosome 5 using a series of polymorphic endogenous retroviruses as genetic markers in backcross mice. The endogenous immunoglobulin heavy chain locus resides on mouse chromosome 12, which shows that transgene isotype switching can occur between two different chromosomes even though normal antibody gene switching has generally been thought to occur within one chromosome. We find that transgene isotype switching involves interchromosomal DNA recombination, and our data suggest that the same enzymatic mechanisms mediate both normal isotype switch recombination and interchromosomal transgene switching. Our findings also support the notion that the isotype switching mechanism can induce chromosomal translocations such as observed for the c- myc gene in some B cell tumors.

Thirty endogenous proviruses belonging to the modified polytropic (Mpmv) class of murine leukemia virus (MLV) were identified by proviral-cellular DNA junction fragment segregation in several sets of recombinant inbred mice. Twenty-six Mpmv loci were mapped to chromosomal regions by matching proviral strain distribution patterns to those of previously assigned genes. Like other endogenous nonecotropic MLVs, Mpmv loci were present on several chromosomes in all strains examined. We pooled recombinant inbred strain linkage data from 110 MLV loci and selected marker genes in order to construct a chromosomal linkage map. Every mouse chromosome was found to harbor at least one proviral insertion, and several regions contained multiple integrations. However, the overall distribution of the 110 mapped proviruses did not deviate significantly from a random distribution. Because of their polymorphism in inbred strains of mice, and the ability to score as many as 57 proviruses per strain using only three hybridization probes, the nonecotropic MLVs mapped in common strains of mice offer a significant advantage over older methods (e.g., biochemical or individual restriction fragment polymorphisms) as genetic markers. These endogenous insertion elements should also be useful for assessing strain purity, and for studying the relatedness of common and not-so-common inbred strains.

There are three known mechanisms by which foreign DNA can be made a permanent part of the genome of an animal cell, and their properties are summarized in this report. Naked DNA introduced into cells is usually rapidly lost, but a small fraction can be integrated by illegitimate recombination, usually accompanied by major and unpredictable rearrangements in both inserted DNA and target. This mechanism, although inefficient and disruptive, accounts for virtually all integrated DNA seen in virus infections, and is often used for making cell lines carrying specific genes as well as transgenic mice. Homologous recombination between inserted and resident DNA is much rarer but can be detected and put to use. The best understood mechanism is that employed by retroviruses and related elements. In contrast to the other mechanisms, retroviral integration results in a predictable, stable association between virus and cell DNA with only minor sequence changes. However, it occurs only when the DNA is derived by reverse transcription of the RNA in an incoming viral particle and contains the correct sequences at its ends. Thus, from a standpoint of vaccine safety, only the first of the three mechanisms is at all relevant. Based on some prior experimentation in animals, the risk of introduction of activated oncogenes or other dangerous sequences by this means is extremely small.

Retroviruses are a highly specialized group of viruses whose members are closely related in genetic organization, virion structure, and mode of replication, yet within this common framework they display an unparalleled diversity of biologic effects on their host. On a large scale, retroviruses have evolved to occupy a wide variety of distinct lifestyles—ranging from a completely benign transposable elementlike association with host germline that can span millennia to horizontal infections that lead to the death of the infected host with lytic, immunologic, or neoplastic disease. On a microscale, retroviruses can often undergo dramatic changes in genome structure during infection of a single host. Examples of this include the reproducible acquisition of oncogenes by slowly oncogenic viruses, the elaborately orchestrated series of recombinations and mutational events that create pathogenic out of benign viruses during the lifetime of certain mice, and the rapid variation in nucleotide sequence seen in the envelope gene of human immunodeficiency virus (HIV) and other lenti viruses.

The ability of human and murine APOBECs (specifically, APOBEC3) to inhibit infecting retroviruses and retrotransposition of some mobile elements is becoming established. Less clear is the effect that they have had on the establishment of the endogenous proviruses resident in the human and mouse genomes. We used the mouse genome sequence to study diversity and genetic traits of nonecotropic murine leukemia viruses (polytropic [Pmv], modified polytropic [Mpmv], and xenotropic [Xmv] subgroups), the best-characterized large set of recently integrated proviruses. We identified 49 proviruses. In phylogenetic analyses, Pmvs and Mpmvs were monophyletic, whereas Xmvs were divided into several clades, implying a greater number of replication cycles between the integration events. Four distinct primer binding site types (Pro, Gln1, Gln2 and Thr) were dispersed within the phylogeny, indicating frequent mispriming. We analyzed the frequency and context of G-to-A mutations for the role of mA3 in formation of these proviruses. In the Pmv and Mpmv (but not Xmv) groups, mutations attributable to mA3 constituted a large fraction of the total. A significant number of nonsense mutations suggests the absence of purifying selection following mutation. A strong bias of G-to-A relative to C-to-T changes was seen, implying a strand specificity that can only have occurred prior to integration. The optimal sequence context of G-to-A mutations, TTC, was consistent with mA3. At least in the Pmv group, a significant 5′ to 3′ gradient of G-to-A mutations was consistent with mA3 editing. Altogether, our results for the first time suggest mA3 editing immediately preceding the integration event that led to retroviral endogenization, contributing to inactivation of infectivity., Author Summary Vertebrate genomes are littered with remnants from earlier retroviral infections, in the form of endogenous retroviruses (ERVs). Cellular host defenses against retroviruses, including the APOBEC3 family of cytidine deaminases, have been described previously. APOBEC3 proteins have been shown to edit some retroviruses and other retrotransposing elements during their replication by deamination of C to U during negative-strand synthesis, resulting in G-to-A mutations in the sense strand. Here, we studied the possible effects that the APOBEC-protein family might have had in the establishing ERVs. We identified 49 endogenous (nonecotropic) murine leukemia viruses, divided into three groups; polytropic, modified polytropic, and xenotropic, in the sequenced C57BL/6J mouse genome. We analyzed genetic variation within and among subgroups and found mutation patterns consistent with APOBEC3 editing of Pmv and Mpmv, but not Xmv proviruses. Evidence such as (i) significantly higher G-to-A mutation frequencies compared to controls and large fractions leading to inactivating stop mutations, (ii) optimal sequence contexts surrounding the mutation positions, and (iii) editing gradient following the time course of retroviral replication, implicate APOBEC3 as a factor contributing to inactivation of these ERVs in the mouse genome.

In this paper we examine genetic relationships of caribou (Rangifer tarandus caribou) in the Aishihik, Chisana, and Wolf Lake herds in the Yukon using DNA fingerprinting. The assignment test used in this analysis showed that the caribou herds were distinct. This finding is consistent with movement data from radio-collared caribou which demonstrates home range fidelity. We found a high level of heterozygosity and a genetic basis for population boundaries. DNA fingerprinting may provide an effective means to compare ecological and genetic relationships.

In recent months, the U.S. National Institutes of Health (NIH) human immunodeficency virus (HIV) vaccine research program has been criticized by a few activists and public health figures who serve on, or have provided testimony to, the President's Advisory Committee on HIV/AIDS (PACHA) (M. Balter