Foamy viruses are complex retroviruses that have been shown to be transmitted from nonhuman primates to humans. In Bangladesh, infection with simian foamy virus (SFV) is ubiquitous among rhesus macaques, which come into contact with humans in diverse locations and contexts throughout the country. We analyzed microsatellite DNA from 126 macaques at six sites in Bangladesh in order to characterize geographic patterns of macaque population structure. We also included in this study 38 macaques owned by nomadic people who train them to perform for audiences. PCR was used to analyze a portion of the proviral gag gene from all SFV-positive macaques, and multiple clones were sequenced. Phylogenetic analysis was used to infer long-term patterns of viral transmission. Analyses of SFV gag gene sequences indicated that macaque populations from different areas harbor genetically distinct strains of SFV, suggesting that geographic features such as forest cover play a role in determining the dispersal of macaques and SFV. We also found evidence suggesting that humans traveling the region with performing macaques likely play a role in the translocation of macaques and SFV. Our studies found that individual animals can harbor more than one strain of SFV and that presence of more than one SFV strain is more common among older animals. Some macaques are infected with SFV that appears to be recombinant. These findings paint a more detailed picture of how geographic and sociocultural factors influence the spectrum of simian-borne retroviruses.

The nonconditional RNA packaging mutant SE21Q1b contains cis-and transacting defects which cause cellular mRNA, rather than viral genomic RNA, to be nonspecifically packaged into SE21Q1b viral particles. Using genomic libraries of the c-SE21Qlb quail cell line, we have been able to construct a molecular clone of the SE21Q1b provirus. Upon transfection into primary quail embryo fibroblasts, the SE21Q1b molecular clone is able to recapitulate the nonspecific RNA packaging phenotype of the c-SE21Q1b cell line. The RNA packaging phenotypes displayed by several SE21Q1b/avian sarcoma-leukemia virus hybrid provirus constructs have further indicated that sequences responsible for the altered RNA packaging phenotype of SE21Q1b are localized in the left third of the SE21Qlb proviral genome. DNA sequence analysis of this region has revealed that the 5' SE21Q1b deletion has removed 179 bp from the SE21Qlb left long terminal repeat and leader regions. Several differences were detected at the carboxyl terminus of the deduced SE21Q1b nucleocapsid protein sequence in comparison with that of Rous sarcoma virus PR-C. Results of site-directed oligonucleotide mutagenesis experiments indicate, however, that the presence of these residues in the nucleocapsid protein alone is not responsible for the decreased RNA packaging specificity of SE21Qlb.

We previously demonstrated that when nonretroviral RNAs are encapsidated in retroviral particles they can be reverse transcribed into cDNAs, which are then integrated into the cellular genome. This transfer of genetic information via retroviral infection has been designated retrofection. Further analyses of three genes transferred in this manner (retrogenes) Several systems have been developed to study the recombination events that result in the acquisition of transferred genes by host cells (9,12,30,41,43); these systems primarily utilize transfection or microinjection to deliver the gene of interest to the host cell. Genes transferred in these ways, however, are frequently integrated as tandem arrays or in multiple sites. More, recently, we and others described systems that allow the study of the integration and expression of single-copy genes (10,22). These studies entail infection of tissue culture cells with retroviral particles containing nonretroviral RNAs and authentic (virally encoded) reverse transcriptase, a process we have called retrofection. In our system (Fig. 1) that harbor single-copy neo genes integrated into the chromosome. This process is RNA mediated and does not appear to require any retroviral sequences in cis, although inclusion of retroviral sequences increases retrofection efficiency.DNA sequences occasionally appear in new genomic locations, both in germ line and somatic cells. In many instances, there is good evidence that these molecules (including certain retrotransposons such as long interspersed nuclear elements and intracisternal A particles) have transposed via RNA intermediates (1). Structural similarities between many of these genes and processed pseudogenes, including the lack of functional transcriptional control sequences and the presence of 3'-terminal poly(dA), have led to the suggestion that processed pseudogenes arose by the integration of cDNAs produced by reverse transcription (39, 49). To evaluate this suggestion and to study the processes involved in the retrovirally mediated transfer of nonretroviral genes, we cloned and sequenced neo retrogenes from three independently derived G418-resistant QT35 clones. Fig. 1). In the case of the mass G418r cultures described in Table 1 and Fig. 7

Newly acquired proviruses related to a mink cell focus-inducing murine leukemia virus were detected in low copy number in restriction endonucleasedigested DNAs from thymic lymphomas of AKR/J mice. These extra proviruses were not present in DNAs of either normal thymus or leukemic brain tissues. Extra tumor-specific DNA fragments generated by restriction endonucleases either were identical in size or fell into similar size classes, suggesting a common site(s) of provirus integration. Characterization of extra EcoRI DNA fragments for mink cell focus-inducing viral sequences revealed that all of them contained large terminal repeat sequences and that a significant number represented proviruses with deletions.

We previously demonstrated that when nonretroviral RNAs are encapsidated in retroviral particles they can be reverse transcribed into cDNAs, which are then integrated into the cellular genome. This transfer of genetic information via retroviral infection has been designated retrofection. Further analyses of three genes transferred in this manner (retrogenes) revealed that each was present in a single copy at a different site in the recipient quail cell genome and included a transcriptional promoter encoded by the encapsidated neo RNA. A unique feature of the retrogenes was a common 16-nucleotide sequence at or near a recombination border, which was not present in either recombination partner. The existence of this sequence suggests a common mechanism of retrogene formation and/or integration mediated by retrofection.