Notes on Genus: Pomovirus

rigid rods
rigid rods

Type member: Potato mop-top virus


General Description

Pomoviruses (from potato mop top virus) had originally been classified with furoviruses but have three genome segments. Where known, the vectors are species of Spongosopora and Polymyxa, root-infecting parasites, classified in the Plasmodiophorales.


Virions rod-shaped, not enveloped. Usually straight with a distinct central canal. Generally of two modal lengths, c.100-150 and 250-300 nm in length, (but difficult to estimate because they are fragile) and about 20 nm in diameter. Symmetry helical. Surface capsomere arrangement obvious. Pitch of helix c. 2.5 nm.


Linear, single-stranded, positive sense RNA in three segments. The 3'-terminus of each RNA has a t-RNA like structure

Genus Genomic Organization

RNA1 encodes the product(s) involved in virus replication as a replicase with a readthrough domain. RNA2 encodes the coat protein and a readthrough domain, while RNA3 contains a triple-gene block (believed to be involved in cell-to-cell movement) and may have an additional small gene. The first sequences determined for PMTV (the type member) were from an isolate with a substantial deletion in the coat protein readthrough. For this reason, some PMTV sequence files and literature have the numbering of RNA2 and RNA3 reversed. In this program, the inconsistency has been corrected and the genome segment of PMTV encoding the coat protein is always described as RNA2.

Type Member Genomic Organization

Based on the full (non-deleted) Swedish sequence, the organisation of the 3 RNAs is:
RNA1 (c. 6050 nucleotides) produces:
1 148 kDa Replication protein with methyltransferase and helicase domains
2 206 kDa Polymerase readthrough, including the RNA-dependent RNA polymerase motif
RNA2 (c. 3100 nucleotides) produces:
7 20 kDaCoat protein
8 91 kDaCoat protein readthrough, involved in fungus transmission; subject to deletion in some isolates
RNA3 (c. 3000 nucleotides) produces:
3 51 kDa3-5 =Triple gene block probably involved in cell-to-cell movement
4 13 kDa
5 21 kDa
6 8 kDaCysteine-rich protein