Conserved structures among the nucleocapsid proteins of the paramyxoviridae: complete nucleotide sequence of human parainfluenza virus type 3 NP mRNA

The nucleotide sequence of the mRNA coding for the nucleocapsid protein (NP) of the paramyxovirus, human parainfluenza virus type 3 (PIV-3), has been determined. The NP mRNA was found to contain 1642 bases, excluding poly(A), and encode a protein of 515 amino acids, with a molecular weight of 57,823. Amino acid residues 1 through 420 of PIV-3 NP protein showed extensive sequence homology with the corresponding amino acids of Sendai virus nucleocapsid protein. There was virtually no homology between the last 95 amino acids. Comparison of the NP proteins of PIV-3, Sendai virus, measles virus, and canine distemper virus revealed, from amino acid residues 160 through 390, some conserved areas between the corresponding proteins of these paramyxoviruses. The 5' terminal sequence of PIV-3 NP mRNA (5'-AGGATTAAAG-3') was similar to the conserved sequence (formula; see text) found at the 5' termini of Sendai virus mRNAs. Both PIV-3 NP and Sendai virus mRNAs had a common 3' terminal tetranucleotide (5'-TAAG-3') preceding the poly (A) tail.     

Fusion glycoprotein of human parainfluenza virus type 3: nucleotide sequence of the gene, direct identification of the cleavage-activation site, and comparison with other paramyxoviruses

The complete sequences of the fusion (F) mRNA and protein of human parainfluenza virus type 3 (PF3) were determined from overlapping cDNA clones. To confirm the cDNA sequence, the complete sequence of the F gene was determined independently by dideoxynucleotide sequencing of genomic RNA using synthetic oligonucleotide primers. The mRNA contains 1845 nucleotides, exclusive of poly (A), has an unusually long (193-nucleotide) 5' nontranslated region, and encodes an F0 protein of 539 amino acids. The site within F0 of the proteolytic cleavage that activates fusion activity was established by direct amino acid sequencing of the NH2 terminus of the F1 subunit. The PF3 F0 protein shares major structural features with the previously sequenced F0 proteins of Sendai virus (murine parainfluenza type 1) and simian virus 5 (SV5, canine parainfluenza type 2), including: similarity in overall length; similarity in location of the site of the activating proteolytic cleavage; the presence of an NH2-terminal signal peptide and COOH-proximal membrane anchor; strong conservation of the sequence at the NH2 terminus of the F1 subunit; and nearly exact conservation in the number and positions of cysteine residues. Alignment of the F0 protein sequences of PF3 with those of Sendai, SV5, and respiratory syncytial virus (RSV) using a matrix that scores both amino acid matches and mismatches provided highly significant statistical evidence that all four proteins are related. The order of decreasing relatedness to PF3 was found to be: Sendai virus, SV5, and RSV.     

The complete nucleotide sequence of turnip mosaic virus RNA Japanese strain

Summary The complete nucleotide sequence of the RNA genome of turnip mosaic virus Japanese strain (TuMV-J) has been determined from five overlapping cDNA clones and by direct sequencing of viral RNA. The RNA sequence was 9833 nucleotides in length, excluding a 3 terminal poly(A) tail. An AUG triplet at position 130–132 was assigned as the initiation codon for the translation of the genome size viral polyprotein which would consist of 3164 amino acid residues. Interestingly, a different amino acid sequence (continuous twenty amino acids) within the cytoplasmic inclusion protein between TuMV-J and Canadian strain of TuMV was observed, caused by an insertion and a deletion of nucleotides.DDBJ/EMBL/GenBank accession number D83184.     

The complete nucleotide sequence of the Popp (1967) strain of Marburg virus: a comparison with the Musoke (1980) strain

Summary The nucleotide sequence of genomic RNA of Marburg virus strain Popp was determined. Strain Popp was isolated in 1967 during the first filoviral outbreak. The virus was purified from blood of infected guinea pigs in which it had been maintained. The length of the determined sequence was 19112 nucleotides. Amino acid sequences of seven known virion proteins were deduced. Nucleotide and amino acid sequences were compared with those of strain Musoke of Marburg virus isolated in 1980 in Kenya and purified from Vero cells. Homology between nucleotide sequences of two strains was 93.9%. Comparisons revealed conserved and variable regions of the nucleotide and amino acid sequences. The GP, the envelope protein of the virion, was found to be the most variable protein. The greatest differences in the protein were located in the supposedly external part of the molecule. Amino acid substitutions in the L protein, the main component of viral RNA-dependent RNA polymerase, were also distributed extremely non-randomly. It was shown that the non-coding regions of the genome were more variable than the coding ones; 37.6% of nucleotide differences corresponded to the former. 72.6% of nucleotide substitutions located in the coding regions were found to be at the third codon position.Presented in part at the Ninth International Conference on Negative Strand Viruses, Estoril, Portugal, October 2–7, 1994 (Abstract 237), and at IXth International Congress of Virology, Glasgow, Scotland, 8–13 August 1993 (Abstract W52-4).     

人副流感病毒广州分离株ZYMgz01全基因组序列测定及分析

目的探讨广州地区副流感病毒的基因组结构和基因型。方法参照GenBank副流感病毒（U51116）全基因组序列设计11对引物,覆盖副流感病毒基因组的全长。以副流感病毒cDNA为模板分段扩增病毒基因组的全长,各片段克隆到T载体上,并进行序列测定和分析。结果人副流感病毒ZYMgz01株全基因组核酸序列为15462bp,提交到GenBank的序列号为EU326526,与3型副流感病毒保守基因同源性为94.0%,具有3型副流感病毒的结构特征。基因组序列同源性比较结果显示,ZHYMgz01株病毒与兰州的LZ22（FJ455842）病毒株的同源性最高,为99.1%;与美国突变病毒株（U51116）同源性为95.1%;与美国病毒株（Z11575）同源性为95.2%;与日本（ABO12132）病毒株的同源性为94.8%,而与加拿大（EU424062）病毒株的同源性为94.8%。系统进化树显示ZHYMgz01病毒株与兰州的LZ22病毒株同属一个进化分支。结论广州地区儿童呼吸道感染的副流感病毒ZHYMgz01全基因组为15462bp,与3型副流感病毒的同源性最高,确定ZHYMgz01是3型副流感病毒。3型副流感病毒系统进化可能与地域差异有一定的关系。     

The complete nucleotide sequence of apple mosaic virus RNA-3

Summary The complete nucleotide sequence of apple mosaic ilarvirus (ApMV) RNA-3 has been determined from cloned viral cDNAs. The 5 terminus of RNA-3 was determined by direct RNA sequencing, while the 3 end was determined by polyadenylation of genomic RNA and sub-cloning using oligo dT. ApMV RNA-3 is 2056 bases in length and encodes at least two open reading frames. It is similar in size and genome organization to the RNA-3 of other members of theBromoviridae, which includes ilarviruses. The CP gene is in the 3 half of the molecule, and another large open reading frame is upstream of the CP gene and can potentially encode a protein of 32 400 daltons. This peptide is the same size and shows limited sequence homology to an open reading frame located at the 5 end of RNA 3 in tobacco streak and prune dwarf ilarviruses and alfalfa mosaic virus, which is postulated to be the viral movement protein. The nucleic acid sequence was not homologous to tobacco streak virus, prune dwarf virus, alfalfa mosaic virus or other members of theBromoviridae. The 5-non-coding region of ApMV RNA-3 contains a 15 base palindromic sequence which encloses a sequence resembling the ICR-2 regions of eukaryotic tRNA gene promoters.     

The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence

The complete genome sequence for an isolate of the Ugandan and Tanzanian strain types of Cassava brown streak virus have been determined using the novel approach of non-directed next generation sequencing. Comparison of the genome sequences revealed that CBSV is highly heterogeneous at the isolate level as well as the strain level. The isolate of the Ugandan strain was found to have a genome 9,070 nucleotides long coding for a polypeptide with 2,902 amino acid residues. The isolate of the Tanzanian strain was 9,008 nucleotides long and coded for a polypeptide with 2,916 amino acid residues. Nucleotide identity between the isolates across the genome was 76%, with protein encoding regions 57–77% and individual proteins had 65–91% amino acid similarity. In addition between the two strains four protein products (PIPO, CI, NIa-Vpg and coat protein) varied in size and an unusual HAM1-like protein, whilst of identical nucleotide length, was found to have the lowest homology. The implication of diversity of CBSV is discussed in the context of speciation, evolution, development of diagnostics, and breeding for resistance.     

The phylogenetic relationship and complete nucleotide sequence of human papillomavirus type 35.

The 7851-bp nucleotide sequence of human papillomavirus (HPV) type 35 was determined. HPV 35 is associated with high-grade cervical intraepithelial neoplasia and invasive carcinomas. From the HPV 35 sequence, open reading frames encoding putative proteins E6, E7, E1, E2, E4, E5, L2, and L1, common to other mucosal HPV types, were identified. Structural and control elements present in the long control region (LCR) conserved among other mucosal HPV types were also present in HPV 35. Analysis of the LCR revealed an additional 20-bp sequence element present in all HPV types associated with malignant proliferation. To further classify HPV 35 with regard to oncogenic potential, phylogenetic analysis of the E6 and E7 proteins from the anogenital HPV types 6, 11, 16, 18, 31, 33, 35, 39, 43, 44, 45, and 51 was performed. This analysis indicated three distinct HPV subgroups; those associated with benign lesions and two branches of those HPV types more often associated with malignant proliferation. HPV 35 is most closely related to HPV types 31 and 16.     

The complete nucleotide sequence of hydrangea ringspot virus

Summary. The complete nucleotide sequence of the genome of the potexvirus, hydrangea ringspot virus, has been determined. The sequence is 6,185 nt in length, excluding the poly (A) tail, and contains six ORFs coding for proteins of 156, 26, 12, 8, 24, and 16 kDa, respectively. ORF 6 is contained within ORF 5 and in this respect the virus is similar to the potexviruses CsCMV, NMV, and SMYEV. Phylogenetic analysis of the putative products of the ORFs and signature motifs contained within these products shows the virus to be most closely related to CsCMV. A similar analysis of data for the coat proteins of potexviruses did not support the previously reported serological relationships between HdRSV and other potexviruses. This is the first complete sequence published for the genome of a potexvirus infecting a dicotyledonous, temperate, deciduous woody species.     

The complete nucleotide sequence of potato virus T

Potato virus T (PVT), a member of an unassigned species in the family Flexiviridae, has a genome 6,539 nt in size with three ORFs coding for replication-associated proteins (185 kDa, ORF 1), movement protein (40 kDa, ORF 2) and coat protein (24 kDa, ORF 3), respectively. PVT differs from the type members of all genera of the family Flexiviridae with a 30K-type movement protein and is phylogenetically distant from all of these viruses, least so from grapevine virus A (GVA, genus Vitivirus), with which it groups in all trees. The viral genome resembles that of trichoviruses but is smaller and does not contain the 3′ terminal fourth ORF found in some members of this genus. PTV may represent a new genus of plant viruses for which the provisional name of Andesvirus is proposed.     

Human infection by a bovine strain of parainfluenza virus type 3

Etiological relationship between a bovine strain of parainfluenza virus type 3 and pneumonia in a child is suggested. Haemagglutination inhibition tests have clearly demonstrated that specific antibodies against the bovine virus were present in the patient's serum. The significance of this finding in relation to human infection is discussed.     

The complete nucleotide sequence of Subterranean clover mottle virus

Summary The complete nucleotide sequence of Subterranean clover mottle virus (SCMoV) genomic RNA has been determined. The SCMoV genome is 4,258 nucleotides in length. It shares most nucleotide and amino acid sequence identity with the genome of Lucerne transient streak virus (LTSV). SCMoV RNA encodes four overlapping open reading frames and has a genome organisation similar to that of Cocksfoot mottle virus (CfMV). ORF1 and ORF4 are predicted to encode single proteins. ORF2 is predicted to encode two proteins that are derived from a –1 translational frameshift between two overlapping reading frames (ORF2a and ORF2b). A search of amino acid databases did not find a significant match for ORF1 and the function of this protein remains unclear. ORF2a contains a motif typical of chymotrypsin-like serine proteases and ORF2b has motifs characteristically present in positive-stranded RNA-dependent RNA polymerases. ORF4 is likely to be expressed from a subgenomic RNA and encodes the viral coat protein. The ORF2a/ORF2b overlapping gene expression strategy used by SCMoV and CfMV is similar to that of the poleroviruses and differ from that of other published sobemoviruses. These results suggest that the sobemoviruses could now be divided into two distinct subgroups based on those that express the RNA-dependent RNA polymerase from a single, in-frame polyprotein, and those that express it via a –1 translational frameshifting mechanism.Received December 17, 2001; accepted April 15, 2003 Published online August 7, 2003     

Interaction between 6/94 virus, a parainfluenza type 1 strain, and human leukocytes.

6/94 virus, a parainfluenza type 1 virus recovered by lysolecithin fusion of multiple sclerosis brain cell cultures with CV-1 cells, replicated in monocyte macrophages and lymphocytes from normal human donors and from a patient with multiple sclerosis. In macrophage cultures, hemadsorption-positive cells and high levels of infectious virus became apparent within 24 to 48 h after infection, persisted for 6 days, and then began to decrease. Phytohemagglutinin-stimulated macrophages yielded similar titers of virus, but the levels were maintained for a longer period of time. Macrophage-produced virus appeared to be infectious for other macrophages in the same culture. Both unstimulated and phytohemagglutinin-stimulated lymphocytes also supported virus replication. Significantly higher titers were produced in the stimulated cultures, T cell-enriched populations producing more virus than unseparated populations whether stimulated or unstimulated. The presence or absence of antibodies to the virus in the donors did not appear to influence the levels of virus obtained in any of the leukocyte cultures. However, an increase in blastic forms after 6/94 virus infection was noted in lymphocytes from donors with antibodies as revealed morphologically and by increased incorporations of tritiated thymidine. Furthermore, 6/94 virus-infected lymphocytes, unlike Sendai virus-infected lymphocytes, were able to respond well to mitogenic stimulation by phytohemagglutinin.     

Konjak mosaic virus: the complete nucleotide sequence of the genomic RNA and its comparison with other potyviruses

Summary. Konjak mosaic virus (KoMV) belongs to the genus Potyvirus, family Potyviridae. The complete nucleotide sequence of KoMV F isolate (KoMV F) was determined. The genome is 9,544 nucleotides long excluding the 3′ terminal poly A tail and encodes a typical potyviral 350-kDa polyprotein of 3,087 amino acids. Phylogenetic analysis using known potyvirus polyproteins shows that KoMV constitutes a branch with yam mosaic virus, close to another branch including Japanese yam mosaic virus, turnip mosaic virus, scallion mosaic virus and lettuce mosaic virus. The 3′ terminal 1,842 nucleotides of a different isolate of KoMV, K-2, was also determined, covering the C-terminal 292 amino acids of the nuclear inclusion protein b (NIb), coat protein (CP), and the 3′ untranslated region. The amino acid sequences of the KoMV F CP and the nucleotide sequences of the KoMV F 3′ untranslated region showed 92.5 and 90.5% identity to the corresponding genes of K-2, 88.7–96.8 and 92.7–94.4% to those of Zantedeschia mosaic virus (ZaMV) isolates, 87.5–89.7% and 85.5–90.3% to those of Japanese hornwort mosaic virus (JHMV) isolates. These results showed that KoMV is a distinct potyvirus and that KoMV, ZaMV, and JHMV are members of the same potyvirus species. Considering that KoMV was the first of these to be described, ZaMV and JHMV may be considered isolates of KoMV.     

Complete nucleotide sequence of the matrix gene of human parainfluenza type 2 virus and expression of the M protein in bacteria

The sequence of the M gene of human parainfluenza virus type 2 (PIV-2) has been determined. The sequence contained a large open reading frame with 1131 nucleotides encoding a protein with a calculated molecular weight of 42,312. Comparison of M protein sequence indicated that PIV-2 was more closely related to mumps virus and Newcastle disease virus than to other parainfluenza viruses, Sendai virus (SV), and parainfluenza virus type 3 (PIV-3), indicating a possible subdividing of the Paramyxovirus into two groups. This grouping is consistent with that obtained from analysis of the HN gene. Measles virus and canine distemper virus definitely belong to the subgroup composed of SV and PIV-3. No homology region was found in all the paramyxoviruses compared. However, a tertiary structure may be conserved in each subgroup of paramyxovirus. The M protein of PIV-2 was expressed in bacteria, and the product was recognized by a monoclonal antibody specific for the PIV-2 M protein. The bacterial-expressed protein, however, was heterogeneous and smaller in size.     

The complete nucleotide sequence of pepper mottle virus genomic RNA: comparison of the encoded polyprotein with those of other sequenced potyviruses.

The complete nucleotide sequence of a pepper mottle virus isolate from California (PepMoV C) has been determined from cloned viral cDNAs. The PepMoV C genomic RNA is 9640 nucleotides excluding the poly(A) tail and contains a long open reading frame starting at nucleotide 168 and potentially encoding a polyprotein of 3068 amino acids. Comparison of the PepMoV C presumptive polyprotein with those of other sequenced members of the potyvirus group, including tobacco etch virus (TEV), tobacco vein mottling virus (TVMV), plum pox virus (PPV), and potato virus Y (PVY), allowed localization of putative protein cleavage sites. A similar analysis was used to determine the position of conserved viral protein-coding regions along the viral genomic RNA. These analyses confirm previous work indicating that genome organization is conserved among members of the genus Potyvirus. The localization of one PepMoV C gene product, the nuclear inclusion body protein a (NIa protein), was analyzed by expressing PepMoV cDNA deletion clones in bacteria and assaying for appearance of mature-sized coat protein, a cleavage product of the NIa protease. Comparative sequence analyses of the putative PepMoV polyprotein with those of TEV, TVMV, PPV, and PVY served to identify regions of the potyviral polyproteins which have diverged within the genus, as well as highly conserved protein features which may play an important functional role in the potyviral life cycle.