Molecular biology of foamy viruses

The full-length sequence of simian foamy virus serotype 2 (SFVmcy-2), isolated from a Taiwanese macaque, was determined. SFVmcy-2 was highly related to SFV serotype 1 (SFVmcy-1), an isolate from the same species, except in the putative receptor binding domain (RBD) in env, which contained novel sequences related to SFV serotype 3 (SFVagm-3), isolated from an African green monkey. The results identify a potential region of neutralization in SFVs and demonstrate recombination between genetically divergent foamy viruses. Simian foamy viruses (SFVs) belong in the Spumavirus genus of the Spumaretrovirinae subfamily of Retroviridae and are widespread in all nonhuman primates (NHPs) (1, 2). SFVs have been isolated from various tissues of different NHPs and were originally designated based upon neutralization serotyping (3). Original foamy virus isolates were designated SFV serotype 1, SFV serotype 2, and SFV serotype 3 (SFV-1, SFV-2, and SFV-3, respectively). These original monkey isolates were renamed to indicate the species of isolation (4): SFV-1, which was isolated from a Taiwanese macaque (Formosan Rock macaque or Macaca cyclopis [mcy]) (5, 6), was designated SFVmac, and SFV-3, which was isolated from an African green monkey (AGM; Chlorocebus aethiops) (7), was designated SFVagm. To distinguish SFVmac/SFV-1 from SFV-2, which was also isolated from M. cyclopis (5), in this paper we have designated these SFVmac viruses SFVmcy-1 and SFVmcy-2, respectively, and the SFVagm virus SFVagm-3 to distinguish it from other AGM isolates. Early results of virus isolation or antibody detection based upon neutralization serotyping showed that, although macaques generally harbor SFVs of serotype 1, viruses with serotype 2 were also present in some cases. In fact, SFVs of both serotype 1 and serotype 2 were isolated from different organs within the same monkey as well as from a single organ (8). AGMs were found to be typically infected with SFVs of serotype 2 and serotype 3, but SFV of serotype 1 was also seen (7-9). More recent molecular studies have also shown that although SFVs generally circulate within a host species, interspecies transmission can occur (10, 11).The biological properties of SFVmcy-1 and SFVagm-3 have been well studied, and whole-genome sequences for both viruses have been determined (6, 12, 13). Our previous studies using a variety of cell lines from different species showed that SFVmcy-2 has a broad host range but different kinetics of replication in different cell lines (14). In this study, we have determined the complete nucleotide sequence of SFVmcy-2 and have determined its genetic relatedness to SFVmcy-1 and SFVagm-3 as well as to other SFVs.The genomic sequence and structure of SFVmcy-2 was determined using virus acquired from the American Type Culture Collection (Manassas, VA) (SFV type 2, catalogue number VR 277, FV-34, lot 4D, 91-10). Full-length SFVmcy-2 sequences were obtained by assembly of cloned DNAs obtained by restriction enzyme digestion (DNA 447) or PCR amplication (DNA 448 and DNA 549) of h...

mentioning

confidence: 99%

Identification of Recombination in the Envelope Gene of Simian Foamy Virus Serotype 2 Isolated from Macaca cyclopis

Galvin

Ahmed

Shahabuddin

et al. 2013

“…The actual details of this mechanism are still largely unknown. However, it appears to be linked to the packaging of another essential component of the infectious viral particle, the viral genomic RNA (29,32). Current data suggest that protein-RNA interaction of both Gag and Pol with viral genomic RNA as well as protein-protein interactions between Gag and Pol are involved in the assembly process (14,21,29).…”

mentioning

confidence: 99%

“…For the Gag proteins of nonprimate FVs, feline FV (FFV), bovine FV (BFV), and equine FV (EFV), no clustering of GR residues is observed, and only small peptide motifs of GR box II (GRII) and GR box III (GRIII) are conserved throughout all FV Gag proteins (25,35,42,43). The GR-rich FV Gag C terminus and, in particular, the clustered GR boxes of primate FVs are thought to play roles in viral replication similar to those of the Cys-His motifs of orthoretroviruses (32).…”

mentioning

confidence: 99%

Novel Functions of Prototype Foamy Virus Gag Glycine- Arginine-Rich Boxes in Reverse Transcription and Particle Morphogenesis

Müllers

Uhlig

Stirnnagel

et al. 2011

122

Prototype foamy virus (PFV) Gag lacks the characteristic orthoretroviral Cys-His motifs that are essential for various steps of the orthoretroviral replication cycle, such as RNA packaging, reverse transcription, infectivity, integration, and viral assembly. Instead, it contains three glycine-arginine-rich boxes (GR boxes) in its C terminus that putatively represent a functional equivalent. We used a four-plasmid replication-deficient PFV vector system, with uncoupled RNA genome packaging and structural protein translation, to analyze the effects of deletion and various substitution mutations within each GR box on particle release, particleassociated protein composition, RNA packaging, DNA content, infectivity, particle morphology, and intracellular localization. The degree of viral particle release by all mutants was similar to that of the wild type. Only minimal effects on Pol encapsidation, exogenous reverse transcriptase (RT) activity, and genomic viral RNA packaging were observed. In contrast, particle-associated DNA content and infectivity were drastically reduced for all deletion mutants and were undetectable for all alanine substitution mutants. Furthermore, GR box I mutants had significant changes in particle morphology, and GR box II mutants lacked the typical nuclear localization pattern of PFV Gag. Finally, it could be shown that GR boxes I and III, but not GR box II, can functionally complement each other. It therefore appears that, similar to the orthoretroviral Cys-His motifs, the PFV Gag GR boxes are important for RNA encapsidation, genome reverse transcription, and virion infectivity as well as for particle morphogenesis.

“…FV replication involves several unique characteristics that distinguish these viruses from the orthoretroviruses (5). An important difference is the expression of FV Pol as a separate precursor protein from a singly spliced mRNA and not as a Gag-Pol fusion protein from unspliced viral genomic RNA (6,7).…”

mentioning

confidence: 99%

“…An important difference is the expression of FV Pol as a separate precursor protein from a singly spliced mRNA and not as a Gag-Pol fusion protein from unspliced viral genomic RNA (6,7). Thus, the FV Pol precursor cannot be packaged into newly forming capsids in an orthoretroviral-like fashion as part of a Gag-Pol fusion protein; instead, FVs directly incorporate the Pol protein into assembling virions (5). Although the mechanism of FV Pol encapsidation is only partially understood, it seems clear that viral RNA (vRNA) is necessary for efficient prototype FV (PFV) Pol particle incorporation (8)(9)(10).…”

mentioning

confidence: 99%

Prototype Foamy Virus Protease Activity Is Essential for Intraparticle Reverse Transcription Initiation but Not Absolutely Required for Uncoating upon Host Cell Entry

Hütter

Müllers

Stanke

et al. 2013

bFoamy viruses (FVs) are unique among retroviruses in performing genome reverse transcription (RTr) late in replication, resulting in an infectious DNA genome, and also in their unusual Pol biosynthesis and encapsidation strategy. In addition, FVs display only very limited Gag and Pol processing by the viral protease (PR) during particle morphogenesis and disassembly, both thought to be crucial for viral infectivity. Here, we report the generation of functional prototype FV (PFV) particles from mature or partially processed viral capsid and enzymatic proteins with infectivity levels of up to 20% of the wild type. Analysis of protein and nucleic acid composition, as well as infectivity, of virions generated from different Gag and Pol combinations (including both expression-optimized and authentic PFV open reading frames [ORFs]) revealed that precursor processing of Gag, but not Pol, during particle assembly is essential for production of infectious virions. Surprisingly, when processed Gag (instead of Gag precursor) was provided together with PR-deficient Pol precursor during virus production, infectious, viral DNA-containing particles were obtained, even when different vector or proviral expression systems were used. Although virion infectivity was reduced to 0.5 to 2% relative to that of the respective parental constructs, this finding overturns the current dogma in the FV literature that viral PR activity is absolutely essential at some point during target cell entry. Furthermore, it demonstrates that viral PR-mediated Gag precursor processing during particle assembly initiates intraparticle RTr. Finally, it shows that reverse transcriptase (RT) and integrase are enzymatically active in the Pol precursor within the viral capsid, thus enabling productive host cell infection.