Complete nucleotide sequence and genome organization of butterbur mosaic virus

Butterbur mosaic virus (ButMV), a member of the genus Carlavirus, was isolated from Japanese butterbur. Here we report the complete nucleotide sequence and genome organization of ButMV. The genome of ButMV consists of 8,662 nucleotides in length and is predicted to contain six ORFs. The ButMV replicase and CP genes share 46.4–54.9 and 43.2–62.1% nucleotide and 38.6–46.6 and 31.3–65.0% amino acid sequence identities, respectively, with those of other carlaviruses. Based on phylogenetic analysis, we suggested that ButMV replicase and CP is most closely related to coleus vein necrosis virus and carnation latent virus, respectively. Together, our results demonstrate that ButMV was a distinct species of the genus Carlavirus.     

Complete genome sequence of switchgrass mosaic virus, a member of a proposed new species in the genus Marafivirus

The complete genome sequence of a virus recently detected in switchgrass (Panicum virgatum) was determined and found to be closely related to that of maize rayado fino virus (MRFV), genus Marafivirus, family Tymoviridae. The genomic RNA is 6408 nucleotides long. It contains three predicted open reading frames (ORFs 1-3), encoding proteins of 227?kDa, 43.9?kDa, and 31.5?kDa, compared to two ORFs (1 and 2) for MRFV. The complete genome shares 76?% sequence identity with MRFV. The nucleotide sequence of ORF2 of this virus and the amino acid sequence of its encoded protein are 49?% and 77?% identical, respectively, to those of MRFV. The virus-encoded polyprotein and capsid protein aa sequences are 83?% and 74-80?% identical, respectively, to those of MRFV. Although closely related to MRFV, the amino acid sequence of its capsid protein (CP) forms a clade that is separate from that of MRFV. Based on the International Committee on Taxonomy of Viruses (ICTV) sequence-related criteria for delineation of species within the genus Marafivirus, the virus qualifies as a member of a new species, and the name Switchgrass mosaic virus (SwMV) is proposed.     

Complete nucleotide sequence of Northern cereal mosaic virus and its genome organization

Summary.  We determined the complete nucleotide sequence, 13, 222 nucleotides (nts) of the Northern cereal mosaic virus (NCMV). The genome had 273 nt 5′ trailer sequence and 90 nts 3′leader sequence. It formed a terminal complementarity in 25 nts of both terminal sequences. A characteristic intergenic sequence (consensus) separating genes, 3′-AUUCUUUUUGACUCUAGU-5′ was presented. The genome had nine open reading frames (ORFs) on the viral complementary sequence. Five putative proteins of NCMV were postulated by its molecular weight or comparison of the similarities to other rhabdovirus proteins: nucleocapsid (N), non-structural protein or phosphoprotein (P), matrix protein (M), glycoprotein (G), and polymerase (L). A series of four small ORFs (genes 3 to 6) were also presented between P and M gene sequences. The proposed NCMV genome organization was 3′leader-N-P-3-4-5-6-M-G-L-5′trailer. N and L proteins of NCMV had low but distinct similarities to those of lettuce necrotic yellows virus and Sonchus yellow net virus, respectively. Received September 29, 1999 Accepted January 26, 2000     

Complete nucleotide sequence of the genome organization of RNA2 of patchouli mild mosaic virus, a new favavirus

Summary.  The complete nucleotide sequence and the genome organization of the RNA 2 of a patchouli mild mosaic virus (PaMMV) was determined. The sequence consists of 3591 nucleotides and contains a single long open reading frame sufficient to code for 118K protein. Three proteins of 52 K, 44 K and 22 K could be encoded by the PaMMV RNA 2 genome. Our analysis of the N-terminal sequences of two species of coat protein (CP) allowed precise location of the CP cistrons within the polyprotein. 44 K and 22 K proteins are the coat proteins. The positions of the cleavage sites are Gln/Ala between 44 K and 22 K coat proteins and Gln/Gly between 52 K and 44 K proteins. Comparison of PaMMV RNA 2 with comoviral and nepoviral RNA 2 showed no sequence similarity. These results as well as previous serological studies strongly suggest that PaMMV is a member in the genus Fabavirus. Received May 29, 1998 Aaccepted July 20, 1998     

Complete nucleotide sequence of rose yellow vein virus, a member of the family Caulimoviridae having a novel genome organization

This report describes the complete nucleotide sequence and genome organization of rose yellow vein virus (RYVV), a proposed new member of the family Caulimoviridae. The RYVV genome is 9314 bp in size and contains eight open reading frames (ORFs). ORFs 1, 2, and 3 have 22–38 % amino acid sequence similarity to known members of the family Caulimoviridae. The remaining ORFs have no significant amino acid sequence similarity to known viruses. Based on differences in its genome organization, its low sequence similarity to known members of the family Caulimoviridae, and the results of phylogenetic analysis, RYVV appears to be a distinct new member of this family.     

Complete nucleotide sequence of rose yellow mosaic virus, a novel member of the family Potyviridae

The complete genomic sequence of rose yellow mosaic virus (RoYMV) was determined and found to have all the features that are characteristic of members of the family Potyviridae. The RoYMV genome is 9508 nucleotides long excluding the 3′-poly-(A) tail and contains a single open reading frame encoding a polyprotein of 3067 amino acids. The RoYMV P3 and CI cistrons are shorter than those of other members of the family Potyviridae, and the 6K1 cistron is completely absent. Comparative sequence analysis revealed that RoYMV had highest amino acid sequence identity across the entire genome sequence to brome streak mosaic virus (33 %) and to turnip mosaic virus (30 %) at the coat protein level. Based on its low sequence similarity to known members of the family Potyviridae and phylogenetic analysis, RoYMV appears to be a distinct, previously undescribed, member of this family.     

The complete genome sequence of Lamium mild mosaic virus, a member of the genus Fabavirus

Lamium mild mosaic virus (LMMV) is the only one of the five members of the genus Fabavirus for which there are no nucleotide sequence data. In this study, the complete genome sequence of LMMV was determined and compared with the available complete genome sequences of other members of the genus Fabavirus. The genome was the largest of the genus but maintained the typical organization, with RNA 1 of 6080 nucleotides (nt), RNA 2 of 4065 nt, and an unusually long 3′ untranslated region in RNA 2 of 603 nt. Phylogenetic analysis of the amino acid sequences of the protease-polymerase (Pro-Pol) region and the two coat proteins confirmed that LMMV belongs to a distinct species within the genus Fabavirus.     

Complete nucleotide sequence of Sesbania mosaic virus: a new virus species of the genus Sobemovirus

Summary.  The complete nucleotide sequence of the Sesbania mosaic virus (SeMV) genomic RNA was determined by sequencing overlapping cDNA clones. The SeMV genome is 4149 nucleotides in length and encodes four potential overlapping open reading frames (ORFs). Comparison of the nucleotide sequence and the deduced amino acid sequence of the four ORFs of SeMV with that of other sobemoviruses revealed that SeMV was closest to southern bean mosaic virus Arkansas isolate (SBMV-Ark, 73% identity). The 5′ non-coding regions of SeMV, SBMV and southern cowpea mosaic virus (SCPMV) are nearly identical. However ORF1 of SeMV which encodes for a putative movement protein of M_r 18370 has only 34% identity with SBMV-Ark. ORF 2 encodes a polyprotein containing the serine protease, genome linked viral protein (VPg) and RNA dependent RNA polymerase domains and shows 78% identity with SBMV-Ark. The N-terminal amino acid sequence of VPg was found to be TLPPELSIIEIP, which mapped to the region 326–337 of ORF2 product and the cleavage site between the protease domain and VPg was identified to be E³²⁵-T³²⁶. The cleavage site between VPg and RNA dependent RNA polymerase was predicted to be E⁴⁴⁵-T⁴⁴⁶ based on the amino acid sequence analysis of the polyprotein from different sobemoviruses. ORF3 is nested within ORF2 in a − 1 reading frame. The potential ribosomal frame shift signal and the downstream stem-loop structure found in other sobemoviruses are also conserved in SeMV RNA sequence, indicating that ORF3 might be expressed via − 1 frame shifting mechanism. ORF4 encodes the coat protein of SeMV, which shows 76 and 66% identity with SBMV-Ark and SCPMV, respectively. Thus the comparison of the non-coding regions and the ORFs of SeMV with other sobemoviruses clearly revealed that it is not a strain of SBMV. Phylogenetic analysis of six different sobemoviruses, including SeMV, suggests that recombination event is not frequent in this group and that SeMV is a distinct member of the genus sobemovirus. The analysis also shows sobemoviruses infecting monocotyledons and dicotyledons fall into two distinct clusters. Received April 20, 2000 Accepted August 28, 2000     

Complete genome sequence of Tunisvirus,a new member of the proposed family Marseilleviridae

Marseillevirus is the founding member of the proposed family Marseilleviridae, which is the second discovered family of giant viruses that infect amoebae. These viruses have been recovered from environmental water samples and, more recently, from humans. Tunisvirus was isolated from fountain water in Tunis, Tunisia, by culturing on Acanthamoeba spp. and is a new marseillevirus. We describe here its 380,011 base-pair genome. A total of 484 proteins were identified, among which 320 and 358 have an ortholog in Marseillevirus and Lausannevirus (e-value <1e-2), respectively, and 259 and 299 have best reciprocal hits with a Marseillevirus and a Lausannevirus protein, respectively. In addition, a significant hit was found in organisms other than marseilleviruses for 144 Tunisvirus proteins, indicating extensive lateral gene transfers, as has been demonstrated previously for Marseillevirus. Finally, a total of 21 ORFans were identified. Phylogeny reconstructions and analysis of the gene repertoires of marseilleviruses, including the proportion of orthologs and the mean amino acid identity between genes in pairs, suggest that the proposed family Marseilleviridae encompasses three lineages. Lineage A is composed of Marseillevirus, Cannes 8 virus and Senegalvirus; lineage B is represented by Lausannevirus alone; and lineage C has Tunisvirus as its first member. Taken together, these findings suggest that the marseilleviruses display a substantial level of diversity.     

Grapevine virus A: nucleotide sequence, genome organization, and relationship in the Trichovirus genus

Summary. The 5′ terminal region of the genomic RNA of grapevine virus A (GVA), a tentative member of the Trichovirus genus, encompassing 5 466 nucleotides, was sequenced. Evidence was obtained that the RNA is capped. Two putative open reading frames (ORF) were identified: ORF 1 that codes for a 194 kDa polypeptide with conserved motifs of replication-related proteins of positive-strand RNA viruses, and ORF 2 that encodes a 19 kDa polypeptide with no significant homology with protein sequences from databases. This polypeptide, however, showed 44% similarity with the product expressed by a comparable ORF present in grapevine virus B (GVB). GVA genome had the same size and structural organization as that of GVB. It also had the same size of the genome of apple chlorotic leaf spot virus (ACLSV), the type species of the Trichovirus genus, but differed substantially in the number (5 versus 3), size, and order of genes. Differences existed also in the degree of sequence homology between polymerases, which did not cluster together in phylogenetic trees. Definitive (ACLSV, PVT) and tentative (GVA, GVB) trichovirus species differ molecularly, biologically and epidemiologically to an extent that warrants the taxonomic revision of the genus. Received June 19, 1996 Accepted September 17, 1996     

Complete sequence of the Pepino mosaic virus RNA genome

We have determined the complete nucleotide sequence (Accession No. AF484251) of the Pepino mosaic virus (PepMV) RNA genome. PepMV is the etiological agent of a new disease which affects tomato crops in Europe and North America. The PepMV genome consists of one single stranded positive sense RNA 6410 nt long that contains five open reading frames (ORFs). ORF 1 is the putative RNA dependent RNA polymerase (RdRp), as it has the characteristic methyltransferase, NTP-binding and polymerase motifs. ORF 2 to 4 form the PepMV triple gene block. ORF 5 codes for the capsid protein. Two short untranslated regions flank the coding regions and there is a poly(A) tail at the 3'end of the genomic RNA. Thus, the genome organization of PepMV is that of a typical member of the genus Potexvirus. The nucleotide sequence obtained shares an overall 99% identity with the genomic RNA of a PepMV isolate from UK which has been partially sequenced. Protein coded by ORF4 is the least conserved between both isolates (95% amino acid identity), whereas proteins coded by ORF3 and ORF5 are identical.     

Helper virus-dependent replication, nucleotide sequence and genome organization of the satellite virus of maize white line mosaic virus

Virus like particles (17 nm in diameter) associated with maize white line mosaic virus (MWLMV) were shown to be a satellite virus of MWLMV (SV-MWLMV) on the basis of the following properties: (1) The SV-MWLMV was dependent upon the presence of MWLMV for replication in maize, while the latter virus could replicate independently of the SV particles. (2) No nucleotide sequence homology was detected between the SV-MWLMV and MWLMV, using complementary DNA probes prepared to the two RNAs, in a Northern blot hybridization analysis. (3) The RNA of the SV-MWLMV translated in vitro to produce a protein of the same Mr (24,000) as that found associated with the SV particles. This protein could be immunoprecipitated with an antiserum to the SV particles. And (4), there was no serological relationship between the coat proteins of MWLMV and the SV-MWLMV. The complete nucleotide sequence of the SV-MWLMV RNA (1168 nucleotides) was determined. The SV-MWLMV RNA contains a single open reading frame encoding a polypeptide of Mr 23,961. Computer analysis revealed no significant homology between SV-MWLMV RNA and any other viral or satellite RNAs. However, the putative SV-MWLMV capsid protein is predicted to share some structural features with the capsid protein of the satellite virus of panicum mosaic virus.     

Complete nucleotide sequence of the cucumber necrosis virus genome

The complete nucleotide sequence of the cucumber necrosis virus (CNV) genome has been determined. The genome is 4701 nucleotides in length and contains five long open reading frames (ORF). ORF1 begins at the first AUG codon at the 5' terminus and terminates at an amber codon. The predicted molecular weight of the polyprotein encoded by ORF1 is 33 kilodaltons (kDa). Readthrough of the ORF1 amber codon would yield a protein with a molecular weight of 92 kDa. Comparison of the amino acid sequence of the 92-kDa protein with the putative replicases of carnation mottle virus (CarMV) and barley yellow dwarf virus (BYDV) shows extensive sequence similarity. This suggests that the CNV 92-kDa protein is the viral replicase and, furthermore, suggests a close evolutionary relationship between CNV, CarMV, and BYDV, members of the Tombus-, Carmo-, and Luteovirus groups, respectively. Immediately following the 92-kDa protein is ORF3 which can encode a 40-kDa protein. It is identified as the coat protein based on its similarity in amino acid composition to the previously determined CNV coat protein sequence (J. H. Tremaine, 1972, Virology 48, 582-590) and on its amino acid sequence similarity with the tomato bushy stunt virus coat protein. Two nested ORFs (ORF4 and -5), in different frames, follow the coat protein gene. Although it is not known if both ORFs are expressed, they would encode proteins with predicted molecular weights of 21 and 20 kDa, respectively.     

The complete nucleotide sequence and genome organization of red clover necrotic mosaic virus RNA-1

The complete nucleotide sequence of red clover necrotic mosaic virus (RCNMV) RNA-1 has been determined. RNA-1 is 3889 nucleotides in length with a 5' terminal m7GpppA cap. The RNA contains three large open reading frames (ORFs): the 5' proximal ORF, encoding a 27-kDa polypeptide; the internal ORF, coding for a 57-kDa polypeptide; and the 3' terminal ORF, encoding the 37-kDa capsid protein. The sequence results confirm in vitro translation of 27-, 50-, and 37-kDa products but do not account for the observed 90-kDa product. A translational frameshift event from the 27- to the 57-kDa ORFs is proposed to explain the synthesis of the observed 90-kDa in vitro product. The putative translational frameshift region is structurally similar to several retrovirus frameshift regions and the putative barley yellow dwarf virus (BYDV) frameshift regions. Extensive amino acid homology was observed in the 57-kDa downstream ORF with the downstream domains of the carnation mottle virus (CarMV), turnip crinkle virus (TCV), maize chlorotic mottle virus (MCMV) readthrough, and BYDV fusion proteins. The 57-kDa ORF contained the conserved "GDD" motif. A significant alignment between the capsid proteins of RCNMV, CarMV, and TCV was also observed. Given the extensive amino acid sequence similarity of RCNMV, CarMV, and TCV polymerase and capsid proteins, we speculate that they are closely related, evolutionarily.