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Most of the genomic sequence of Chara australis virus (CAV), previously called Chara corallina virus, has been determined. It is a ssRNA molecule of 9065 nt with at least four ORFs. At its 5' end is an ORF encoding a protein of 227 kDa, distantly homologous to the multifunctional replicases of benyviruses and rubiviruses. Next is an ORF encoding a protein of 44 kDa, homologous to the helicases of pestiviruses. The third ORF encodes an unmatched protein of 38 kDa that is probably a movement protein. The fourth and 3'-terminal ORF encodes a protein of 17.7 kDa homologous to the coat proteins of tobamoviruses. The short methyltransferase region of the CAV replicase matches only the C-terminal motif of benyvirus methyltransferases. This and other clues indicate that approximately 11% and 2% of the 5' and 3' termini of the complete CAV genome, respectively, are missing from the sequence. The aligned amino acid sequences of the CAV proteins and their nearest homologues contain many gaps but relationships inferred from them were little affected by removal of these gaps. Sequence comparisons show that three of the CAV genes may have diverged from the most closely related genes of other viruses 250-450 million years ago, and the sister relationship between the genes of CAV and those of benyviruses and tobamoviruses, mirroring the ancient sister relationship between charophytes (i.e. the algal host of CAV) and embryophytes (i.e. the plant hosts of tobamoviruses and benyviruses), is congruent with this possibility.

The consensus secondary structure of the virion proteins (VPs) of tymoviruses was predicted from their amino acid sequences using a combination of computer methods: profile alignment, hydrophobicity moment and 'PredictProtein'. All methods predicted that they were eight-stranded anti-parallel beta-barrels with two alpha-helical regions. The predicted structure was used to design recombinants of turnip yellow mosaic virus (TYMV) in which selected parts of its VP were replaced with homologous regions of belladonna mottle virus (BeMV) in a cDNA clone encoding the genome of TYMV. Six of ten such recombinants were fully viable and most gave symptoms in Chinese cabbage indistinguishable from those of TYMV, although they did not always infect plants systemically and none infected hosts of BeMV or of other tymoviruses. A TYMV recombinant with the N-terminal part of its VP replaced with the E71 epitope of Plasmodium falciparum was also viable, but others with the same region replaced with the V3 region of the lentivirus human immunodeficiency virus type 1 were not. Epitope analysis of antisera prepared against the virions of parental TYMV and some of the recombinants showed that, although the N terminus of the VP is immunogenically dominant, it is not exposed at the surface of the virion, a finding confirmed by comparing the electrophoretic mobilities of the virions. The recently published structure of the TYMV VP determined by X-ray crystallography confirms the accuracy of the predicted secondary structure of the VP, and hence the utility of the methods used.

The complete genomic sequence of cardamine chlorotic fleck carmovirus (CCFV) has been determined. The genome is a positive-sense ssRNA molecule 4041 nucleotides in length, and has 47 to 64% sequence identity with turnip crinkle, carnation mottle and melon necrotic spot carmoviruses. CCFV and these other carmoviruses have four similar open reading frames (ORFs), and CCFV has large regions of amino acid identity in all of these ORFs with a European isolate of turnip crinkle virus. CCFV, which replicates well in Arabidopsis thaliana, has only been found so far in Australia in the wild perennial brassica Cardamine lilacina.