Complete nucleotide sequence of the genomic RNA of Sindbis virus

The entire nucleotide sequence of the genomic RNA of the type virus of the alphavirus genus, Sindbis virus, has been determined. The genome is 11,703 nucleotides in length, exclusive of the 5' cap and the 3'-terminal poly(A) tract. After the 5'-terminal cap there are 59 nucleotides of 5' nontranslated nucleic acid followed by a reading frame of 7539 nucleotides that encodes the nonstructural polypeptides and which is open except for a single opal termination codon. Following 48 untranslated bases located in the junction region which separates the nonstructural and structural protein coding sequences, there is an open reading frame 3735 nucleotides long that encodes the structural proteins. Finally, the 3' untranslated region is 322 nucleotides long. The nonstructural proteins are translated from the genomic RNA as two polyprotein precursors. The first is 1896 amino acids in length and terminates at an opal codon at position 1897. This polyprotein is processed to produce three polypeptides called nsP1, nsP2, and nsP3. Sites of post-translational cleavage to produce these three proteins have been tentatively located using available N-terminal amino acid sequence data. In both cases cleavage probably occurs between the two alanine residues in the sequence Gly-Ala-Ala. The fourth nonstructural protein, nsP4, is produced when readthrough of the opal codon produces a second polyprotein precursor of length 2513 amino acids, which is also cleaved posttranslationally. The structural proteins are translated from a subgenomic message which begins at nucleotide 7598, is 4106 nucleotides in length (exclusive of the poly(A) tract), and is coterminal with the 3' end of the genomic RNA. The structural proteins are also translated as a polyprotein precursor which is cleaved to produce a nucleocapsid protein and two integral membrane glycoproteins as well as two small peptides not present in the mature virion. A replication strategy for Sindbis virus based upon the complete nucleotide sequence, as well as prior data, is presented.     

Complete nucleotide sequence of four RNA segments of fig mosaic virus

The complete sequence of four viral RNA segments of fig mosaic virus (FMV) was determined. Each of the four RNAs comprises a single open reading frame (ORF) 7,093, 2,252, 1,490 and 1,472 nucleotides in size, respectively. These ORFs encode the following proteins in the order: RNA-dependent RNA polymerase (p1 264 kDa), a putative glycoprotein (p2 73 kDa), a putative nucleocapsid protein (p3 35 kDa) and a protein with unknown function (p4 40.5 kDa). All RNA segments possess untranslated regions containing at the 5′ and 3′ termini a 13-nt complementary sequence. A conserved motif denoted premotif A was found to be present in addition to the five RdRp motifs A–F in RNA-1. In phylogenetic trees constructed with the amino acid sequences of RNA-1 and RNA-2, FMV clustered consistently with European mountain ash ringspot-associated virus (EMARaV) in a clade close to those comprising members of the genera Hantavirus, Orthobunyavirus and Tospovirus. The amino acid sequence of the putative FMV nucleocapsid protein encoded by RNA-3 shared identity with comparable sequences of EMARaV and the unclassified viruses pigeonpea sterility mosaic virus (PPSMV) and maize red stripe virus (MRSV). The nucleocapsid sequences rooted the four viruses in a clade close to the genus Tospovirus. Based on molecular, morphological and epidemiological features, FMV appears to be very closely related to PPSMV and MRSV. All these viruses are phylogenetically related to EMARaV and therefore seem to be eligible for classification in the proposed genus Emaravirus, which, in turn, may find a taxonomic allocation in the family Bunyaviridae.     

Complete nucleotide sequence of wheat yellow mosaic bymovirus genomic RNAs

Summary.  The complete sequences of wheat yellow mosaic bymovirus (WYMV) RNA1 and RNA2 were determined. RNA1 is 7 636 nucleotides long [excluding the 3′-poly(A)], and codes for a 269 kDa polyprotein of 2 404 amino acids which contains the capsid protein (CP) at the C terminus and seven putative non-structural proteins. RNA2 is 3 659 nucleotides long and codes for a polyprotein of 904 amino acids which contains a 28 kDa putative proteinase and a 73 kDa polypeptide. These functional proteins are arranged as in RNA1 and RNA2 of barley yellow mosaic bymovirus (BaYMV). Comparisons with the sequence reported for the 3′ half of RNA1 of wheat spindle streak mosaic bymovirus (WSSMV) from Southern France show that WYMV and WSSMV have a similar genetic organization. However, WYMV and WSSMV share only 77% amino acid sequence identity in their deduced CPs in spite of their close serological relationship, and 74% nucleotide sequence identity in their 3′ non-coding regions. Thus, the sequence data indicate that WYMV and WSSMV are not strains of the same virus, which has long been suggested, but are distinct virus species within the genus Bymovirus of the family Potyviridae. Accepted December 19, 1997 Received November 14, 1997     

Complete nucleotide sequence of Nootka lupine vein-clearing virus

The complete genome sequence of Nootka lupine vein-clearing virus (NLVCV) was determined to be 4,172 nucleotides in length containing four open reading frames (ORFs) with a similar genetic organization of virus species in the genus Carmovirus, family Tombusviridae. The order and gene product size, starting from the 5'-proximal ORF consisted of: (1) polymerase/replicase gene, ORF1 (p27) and ORF1RT (readthrough) (p87), (2) movement proteins ORF2 (p7) and ORF3 (p9), and, (3) the 3'-proximal coat protein ORF4, (p37). The genomic 5'- and 3'-proximal termini contained a short (59 nt) and a relatively longer 405 nt untranslated region, respectively. The longer replicase gene product contained the GDD motif common to RNA-dependent RNA polymerases. Phylogenetically, NLVCV formed a subgroup with the following four carmoviruses when separately comparing the amino acids of the coat protein or replicase protein: Angelonia flower break virus (AnFBV), Carnation mottle virus (CarMV), Pelargonium flower break virus (PFBV), and Saguaro cactus virus (SgCV). Whole genome nucleotide analysis (percent identities) among the carmoviruses with NLVCV suggested a similar pattern. The species demarcation criteria in the genus Carmovirus for the amino acid sequence identity of the polymerase (<52%) and coat (<41%) protein genes restricted NLVCV as a distinct species, and instead, placed it as a tentative strain of CarMV, PFBV, or SgCV when both the polymerase and CP were used as the determining factors. In contrast, the species criteria that included different host ranges with no overlap and lack of serology relatedness between NLVCV and the carmoviruses, suggested that NLVCV was a distinct species. The relatively low cutoff percentages allowed for the polymerase and CP genes to dictate the inclusion/exclusion of a distinct carmovirus species should be reevaluated. Therefore, at this time we have concluded that NLVCV should be classified as a tentative new species in the genus Carmovirus, family Tombusviridae.     

Complete genomic nucleotide sequence and analysis of the temperate bacteriophage VWB

The entire double-stranded DNA genome of the Streptomyces venezuelae bacteriophage VWB was sequenced and analyzed. Its size is 49,220 bp with an overall molar G + C content of 71.2 mol%. Sixty-one potential open reading frames were identified and annotated using several complementary bioinformatics tools. Clusters of functionally related putative genes were defined, supporting a refined version of the modular theory of phage evolution.     

Complete nucleotide sequence of cherry necrotic rusty mottle virus

Summary.  A virus closely related to cherry green ring mottle virus (CGRMV) was isolated from a tree displaying typical symptoms of cherry necrotic rusty mottle disease. We have named this virus cherry necrotic rusty mottle virus (CNRMV) and report here its complete genomic sequence as determined from overlapping cloned cDNAs. CNRMV has a genome of 8,432 nucleotides excluding the 3′ poly(A) sequence and codes for 7 significant open reading frames (ORFs). Five of these ORFs are conserved among all fovea-, allexi-, potex- and carlaviruses and code for a methyltransferase/helicase/polymerase polypeptide, the triple gene block movement proteins and the coat protein. Two further ORFs, ORFs 2a and 5a, are nested completely within ORFs 2 and 5, respectively. The putative translation products from these ORFs display sequence similarity with putative translation products from two similarly nested ORFs present in the CGRMV genome. The function of these two ORFs is unknown, nor are they conserved among other related viruses. Received April 21, 2000 Accepted July 6, 2000     

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.     

Complete nucleotide sequence and affinities of the genomic RNA of Narcissus common latent virus (genus Carlavirus)

Summary. The complete sequence of an isolate of Narcissus common latent virus (NCLV) from Zhangzhou city, Fujian, China was determined from amplified fragments of purified viral RNA. Excluding the poly(A) tail, the genomic RNA of NCLV was 8539 nucleotides (nt) long and had the typical organization for a member of the genus Carlavirus. The most closely related species were Potato virus M, Hop latent virus and Aconitum latent virus, which had 58–59% nt identity to NCLV in their entire genomes. These relationships were confirmed by a phylogenetic analysis using a composite nucleotide alignment of all the open reading frames.     

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 nucleotide sequence of the duck plague virus gE gene

Archives of Virology -     

Complete nucleotide sequence of the Japanese encephalitis virus genome RNA

The complete nucleotide sequence of the Japanese encephalitis virus (JEV) genome RNA was determined. The JEV genome contains 10,976 nucleotides and encodes a single long open reading frame (ORF) of 10,296 nucleotides corresponding to 3432 amino acid residues. This long polypeptide is thought to be cleaved into three structural proteins and several nonstructural proteins of the virus. The genetic location of the three structural proteins was determined by comparing the deduced amino acid sequence from the nucleotide sequence with the N-terminal amino acid sequences that were determined from the three purified structural proteins. The C-terminal region of the ORF may encode a RNA-dependent RNA polymerase which has significant sequence homology with those of other RNA viruses.     

Complete nucleotide sequence of dengue type 3 virus genome RNA

The complete nucleotide sequence of the genome of the dengue virus type 3 was determined. Sequence analyses of the genomic RNA and cloned cDNA revealed that the genomic RNA contains 10,696 nucleotides and encodes a single open reading frame of 10,170 nucleotides corresponding to 3390 amino acid residues. The N-terminal amino acid sequences of three structural proteins (C, M, and E proteins) and the preM protein were also determined from the purified virion. When the deduced amino acid sequence and N-terminal amino acid sequence determined from purified proteins were compared with those of other flaviviruses, the genome organization was found to be the same as that of other flaviviruses.     

Conserved nucleotide sequence of rabies virus cDNA encoding the nucleoprotein

The cDNAs of rabies virus (the CVS strain) encoding the structural proteins (G, N, NS, and M) were cloned. Of these clones, the nucleotide sequence of the cDNA encoding the nucleoprotein was determined to compare with those of other strains of rabies virus. The comparison confirmed that the nucleotide sequences and deduced amino acid sequences are highly conserved among strains including an avirulent strain.     

Complete nucleotide sequence and genomic organization of a primate calicivirus, Pan-1

Summary.  The primate calicivirus, Pan-1, was originally isolated from several primate species. It displayed typical calicivirus morphology by electron micro-scopy. We determined the genomic sequence of Pan-1 by cDNA cloning and direct RNA sequencing. Pan-1 shares a similar genomic organization and a high degree of sequence identity with feline caliciviruses. The Pan-1 genome contains 8 304 nucleotides, plus a poly-A tail, and is longer than any other calicivirus strains with a completely known sequence. The extra sequences of Pan-1 include a unique 424-nucleotide sequence at the 5′ end of ORF1, additional amino acids at the N-terminus of the capsid, and a longer 3′ UTR. Received March 20, 1998 Accepted July 22     

Complete nucleotide sequence of the genomic RNA of a Japanese yam mosaic virus, a new potyvirus in Japan

Summary.  We determined the complete nucleotide sequence of a potyvirus purified from a Japanese yam plant. The genomic RNA of this virus is 9 757 nucleotides (nts) in length, excluding the 3′-terminal poly(A) tail. It contains a single open reading frame (ORF) encoding a polyprotein of 3130 amino acids (aa) with a calculated Mr of 356,793. The genomic organization of this potyvirus is similar to that of other members of the genus Potyvirus and nine potential cleavage sites for the viral proteinase were found by comparison of its sequence with those available for other potyviruses. The nucleotide sequence and genome characteristics show that this isolate is a new potyvirus species. Its polyprotein differs substantially from Yam mosaic virus (YMV) (50% amino acid sequence identity) and fourteen other potyvirus species examined (44–59% identity). Although this potyvirus has been classified as YMV, our results suggest that the potyvirus infectious to the Japanese yam plant in Japan is distinct from YMV. Therefore, we propose that the Japanese yam potyvirus should be designated as Japanese yam mosaic virus (JYMV). September 14, 1998 Received August 3, 1998