# ICTV Virus Taxonomy Profile: Pseudoviridae

Carlos Llorens, Beatriz Soriano, Mart Krupovic, Ictv Report Consortium

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Carlos Llorens, Beatriz Soriano, Mart Krupovic, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Pseudoviridae. Journal of General Virology, 2021, 102 (3), pp.001563. 10.1099/jgv.0.001563. pasteur-03188402

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# ICTV Virus Taxonomy Profile: *Pseudoviridae*

Carlos Llorens¹*, Beatriz Soriano¹, Mart Krupovic²* and ICTV Report Consortium

## Abstract

*Pseudoviridae* is a family of reverse-transcribing viruses with long terminal repeats (LTRs) belonging to the order *Ortervirales*. Pseudoviruses are commonly found integrated in the genomes of diverse plants, fungi and animals and are broadly known as Ty1/Copia LTR retrotransposons. Inside the cell, they form icosahedral virus particles, but unlike most other viruses, do not have an extracellular phase. This is a summary of the ICTV Report on the family *Pseudoviridae*, which is available at *ictv.global/report/pseudoviridae*.

<table><caption>**Table 1.** Characteristics of members of the family *Pseudoviridae*</caption><thead><tr><th>Example:</th><th>Saccharomyces cerevisiae Ty1 virus (M18706), species Saccharomyces cerevisiae Ty1 virus, genus Pseudovirus</th></tr></thead><tbody><tr><td>Virion</td><td>Virions are icosahedral (T=3 or 4) and might be enveloped</td></tr><tr><td>Genome</td><td>Two identical copies of linear single-stranded RNA</td></tr><tr><td>Replication</td><td>Replication by reverse transcription primed with a host-encoded tRNA</td></tr><tr><td>Translation</td><td>Genomic RNA is translated into one or more polyproteins</td></tr><tr><td>Host range</td><td>Fungi, plants and animals</td></tr><tr><td>Taxonomy</td><td>Realm Riboviria, kingdom Pararnavirae, phylum Artverviricota, class Revtraviricetes, order Ortervirales, family Pseudoviridae; the genera Pseudovirus, Hemivirus and Sirevirus include >30 species</td></tr></tbody></table>

## VIRION

Pseudoviruses form intracellular, somewhat irregularly shaped virus-like particles (VLPs) 30–40 nm in diameter, which do not display infectivity and remain intracellular (Table 1). VLPs are formed by self-assembly of proteins encoded by the *gag* gene, namely the capsid (CP) and nucleocapsid (NC) proteins, which are homologous to the equivalent proteins of retroviruses and other members of the order *Ortervirales* [1]. Expression of truncated Gag protein variants yields icosahedral VLPs of different diameters but with a mean radius of 20 nm built on the *T*=3 or *T*=4 lattice (Fig. 1) [2, 3].

## GENOME

The genome of pseudovirids ranges from 4 kb to >9 kb and has an internal region flanked by two identical non-coding

sequences called long terminal repeats (LTRs) (Fig. 2). LTRs are variable in size and contain three regions, named U3-R-U5 in analogy to retroviral LTRs. U3 contains promoters, R is repeated on each end of the transcript, and U5 constitutes the first portion of the reverse-transcribed genome. The internal region is delimited by two short motifs: the primer binding site (PBS), which is located downstream of the 5'-LTR and is usually complementary to the initiator tRNA<sup>Met</sup>, and the polypurine tract (PPT), which is upstream of the 3'-LTR. The internal region may contain one (*gag-pol*), two (*gag* and *pol*) or three (*gag*, *pol* and *env*) ORFs. The Gag polyprotein includes domains for the CP and NC proteins, while Pol includes domains for the protease (PR), integrase (INT) and reverse transcriptase-ribonuclease H (RT-RH). Members of the genus *Sirevirus* carry a third ORF downstream of *gag-pol* encoding a putative envelope protein [4].

Received 23 December 2020; Accepted 15 January 2021; Published 02 February 2021

**Author affiliations:** ¹Biotechvana, Scientific Park University of Valencia, 46980, Paterna, Valencia, Spain; ²Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France.

*Correspondence: Carlos Llorens, carlos.llorens@biotechvana.com; Mart Krupovic, mart.krupovic@pasteur.fr

Keywords: *Pseudoviridae*; ICTV Report; taxonomy.

Abbreviations: CP, capsid; INT, integrase; LTR, long terminal repeat; NC, nucleocapsid; PBS, primer binding site; PPT, polypurine tract; PR, protease; RH, ribonuclease H; RT, reverse transcriptase; VLP, virus-like particles.

001563 © 2021

<figure><img src="image_3.png" /></figure>
<figure><img src="image_4.png" /><figcaption>**Fig. 1.** Saccharomyces cerevisiae Ty1 virus particles formed from truncated capsid protein (aa 1–381). The surface structures of two forms (T=3, left; T=4, right) of around 30–40 nm determined by cryo-electron microscopy, are flanked by the corresponding schematic models. (Courtesy of H. Saibil, adapted from [3] with permission from American Society for Microbiology.)</figcaption></figure>

## REPLICATION

The replication of pseudovirids resembles that of retroviruses and occurs via reverse transcription in the VLP. The cellular tRNA molecule, typically initiator tRNA<sup>Met</sup>, which is packaged into the VLP, anneals to the viral RNA genome at the PBS complementary to the 3'-end of that tRNA and is used by RT as a primer to start reverse transcription. Once the full-length proviral cDNA is synthetized, it is imported into the nucleus, where it is integrated into a chromosomal target site by INT. The integrated form (equivalent to the retroviral provirus) is transcribed by the host RNA polymerase II to generate a new viral RNA molecule, which is translated to produce the Gag and Pol polyproteins and is packaged into the VLPs to reinitiate the replication cycle.

## TAXONOMY

Current taxonomy: **ictv.global/taxonomy**. The family *Pseudoviridae* belongs to the order *Ortervirales* [5] and includes the genera *Pseudovirus*, *Hemivirus* and *Sirevirus*. Current classification is based on host tropism, gene content and the length of the tail of the tRNA used as a primer to initiate reverse transcription. Hemiviruses differ from members of the genus *Pseudovirus* in that they use only a short segment of the tRNA. By contrast, sireviruses are restricted to plants and mostly encode a protein equivalent to retroviral Env downstream of the *gag-pol* gene [4]. Further updates and revisions in the genus demarcation of pseudovirids are expected to be based on phylogenetic criteria as described in the full ICTV Report (see Resources).

## RESOURCES

Full ICTV Report on the family *Pseudoviridae*: ictv.global/report/pseudoviridae.

<figure><img src="image_5.png" /><figcaption>**Fig. 2.** Pseudovirid genome organization. LTRs are white and show labels for the U3, R and U5 regions. Other labels are: capsid (CP); integrase (INT); long terminal repeat (LTR); nucleocapsid (NC); polypurine tract (PPT); primer binding site (PBS); protease (PR); reverse transcriptase (RT); ribonuclease H (RH); surface (SU); transmembrane (TM).</figcaption></figure>

Gypsy Database (GyDB) devoted to viruses and mobile genetic elements: http://gydb.org.

### Funding information

B.S. was supported by the pre-doctoral research fellowship from Industrial Doctorates of MINECO (Grant 659 DI-17-09134). Production of this Profile, the ICTV Report, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA).

### Acknowledgements

Members of the ICTV Report Consortium are Stuart G. Siddell, Andrew J. Davison, Elliot J. Lefkowitz, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Richard J. Orton and Balázs Harrach.

### Conflicts of interest

The authors declare that there are no conflicts of interest.

### References

1. Krupovic M, Koonin EV. Homologous capsid proteins testify to the common ancestry of retroviruses, caulimoviruses, pseudoviruses, and metaviruses. *J Virol* 2017;91:e00210-17.

2. Burns NR, Saibil HR, White NS, Pardon JF, Timmins PA et al. Symmetry, flexibility and permeability in the structure of yeast retrotransposon virus-like particles. *EMBO J* 1992;11:1155-1164.

3. Palmer KJ, Tichelaar W, Myers N, Burns NR, Butcher SJ et al. Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles. *J Virol* 1997;171:6863-6868.

4. Peterson-Burch BD, Wright DA, Laten HM, Voytas DF. Retroviruses in plants? *Trends Genet* 2000;16:151-152.

5. Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H et al. *Ortervirales*: new virus order unifying five families of reverse-transcribing viruses. *J Virol* 2018;92:e00515-18.