Notes on Genus: Nepovirus

icosahedra

Type member: Tobacco ringspot virus

Contents

• Members of this Genus
• General Description
• Morphology
• Electron Micrograph
• Genome
• Genus Genomic Organization
• Genome Map
• Type Member Genomic Organization
• All Known Sequences
• Curated Sequences

General Description

The genus Nepovirus (nematode transmitted polyhedral viruses) is one of 3 genera in the subfamily Comovirinae of the plant picornavirus family Secoviridae. In common with other genera in the subfamily, its members are characterised by their bipartite genome encapsidated in icosahedral particles with each genome segment producing a polyprotein. Nematode transmission distinguish the members from those in other genera of the family. Their genomes are also larger than those in other genera.

Morphology

Virions isometric (icosahedral), not enveloped, of two types but similar in size (about 28 nm in diameter) and appearance. Nucleocapsids appear to be angular. Incomplete virus particles (empty capsids) are often present (T component).

Virions composed of 27-40 % nucleic acid (M component), or 42-46 % nucleic acid (B component).

Genome

Bipartite, linear, single stranded, positive sense RNA. The genome segments are encapsidated separately into different types of particles: RNA1 (c. 8000 nucleotides) occurs as a single copy in each B type virion and RNA2 (c. 4000-7000 nucleotides) usually as a single copy in each M virion but two copies may be present if RNA2 is smaller than 4kb. The 3' terminus of each RNA has a poly(A) tract and the 5' terminus has a genome-linked protein (VPg).

Genus Genomic Organization

Each RNA is translated into a polyprotein, which is then processed by a series of steps into functional proteins: RNA1 encodes proteins necessary for replication while the coat protein and cell-to-cell movement products are encoded on RNA2. The full details for the type member are not available, but the products of beet ringspot virus are as follows:

RNA1 produces a polyprotein of 254 kDa processed into 5 peptides:
1.	63 kDa	Processing regulator (protease co-factor)
2.	72 kDa	Nucleotide binding protein with helicase activity
3.	2.3 kDa	VPg: genome-linked protein
4.	23 kDa	Protease
5.	92 kDa	Polymerase
RNA2 produces a polyprotein of 150 kDa processed into 2 functional peptides:
1.	93 kDa	Movement protein
2.	57 kDa	Coat protein

Type Member Genomic Organization

RNA1 (7514 nt) produces a polyprotein of 257 kDa that is probably processed into 5 peptides:
1.	Processing regulator (protease co-factor)
2.	Nucleotide binding protein with helicase activity
3.	VPg: genome-linked protein
4.	Protease
5.	Polymerase
RNA2 (3929 nt) produces a polyprotein of 122 kDa that is probably processed into 2 or 3 functional peptides with the coat protein at the C-terminus