Sequence analysis of the fragment of the phosphoprotein gene of Polish distemper virus isolates

Summary. The nucleotide sequence analysis of the 429bp fragment of the P gene of 11 Polish field isolates of Canine distemper virus (CDV), reference strains and other virus isolates available in the GenBank was the aim of the studies. High homology between all dog strains from east-southern region of Poland and reference strains of CDV was demonstrated. It was estimated as 97–100% for CDV-OND; 96.7–99.8% for CDV-Rock; 96.7–99.8% for CDV-LED and 96.3–97.9% for A75-17. The 100% homology of the nucleotide sequence was observed between CDV Pulawy 92, CDV Pulawy 97 and the reference CDV-OND. The homology between CDV-OND and viruses isolated from the mink and ferret was estimated as 97.7% and 98.4%, respectively. Virus strains isolated from blue foxes demonstrated the highest homology to CDV-OND – equal to 97.7% for DV 79 and 99.5% for DV 92. The fox isolate from 1992 had higher level of homology to dog isolates (96.5–99.5%) than the strain isolated from the fox in 1979 (97.2–98.8%). The phylogenetic tree has two main lineages representing two separated genetic groups: I containing PDV and II containing all distemper virus strains isolated from terrestrial carnivores. CDV strains isolated from dogs from Pulawy region between 1992–1998 and from the fox (DV 92) formed the separate lineage containing also reference strains. They differed from the native isolates from the mink and ferret as well as from Japanese strains of CDV.Received October 29, 2002; accepted April 2, 2003 Published online June 11, 2003     

Messenger RNA encoding the phosphoprotein (P) gene of human parainfluenza virus 3 is bicistronic

The complete nucleotide sequence of the phosphoprotein (P) mRNA of human parainfluenza virus 3 (PIV-3) was derived from two cDNA clones spanning almost the entire P gene. The mRNA, excluding the poly(A) tail, is 2014 nucleotides long and is bicistronic. The first open reading frame (ORF) codes for the phosphoprotein (P) of mol wt 68,860. Seven nucleotides downstream from the first AUG codon, in a +1 reading frame, there is an additional ORF which can code for a polypeptide of mol wt 23,266. The latter protein appears to be similar to the C proteins found in cells infected with several paramyxoviruses. Comparison of the predicted amino acid sequence of the P and C proteins of PIV-3 with the corresponding Sendai virus proteins reveals considerable homology at the C-terminal half. In contrast, the P and C proteins of PIV-3 share very little homology with the measles virus P and C proteins, respectively.     

Sequence analysis of the phosphoprotein (P) genes of human parainfluenza type 4A and 4B viruses and RNA editing at transcript of the P genes: the number of G residues added is imprecise

We cloned and sequenced the cDNAs against genomic RNAs and mRNAs for phosphoproteins (Ps) of human parainfluenza virus types 4A (PIV-4A) and 4B (PIV-4B). The PIV-4A and -4B P genes were 1535 nucleotides including poly(A) tract and were found to have two small open reading frames, neither of which was apparently large enough to encode the P protein. A cluster of G residues was found in genomic RNA and the number of G residues was 6 in both PIV-4A and -4B. However, the number of G residues at the corresponding site in the mRNAs to the genomic RNA was not constant. Three different mRNA cDNA clones were obtained; the first type of mRNA encodes a larger (P) protein of 399 amino acids, the second type encodes V protein of 229 or 230 amino acids, and the third type encodes the smallest protein (156 amino acids). Comparisons on the nucleotide and the amino acid sequences P and V proteins between these two subtypes revealed extensive homologies. However, these homology degrees are lower than that of NP protein. The C-terminal regions of the P and V proteins of PIV-4s could be aligned with all other Paramyxoviruses, PIV-2, mumps virus (MuV), simian virus 5 (SV 5), Newcastle disease virus (NDV), measles virus (MV), canine distemper virus (CDV), Sendai virus (SV), and PIV-3. On the other hand, the P-V common (N-terminal) regions showed no homology with MV, CDV, SV, and PIV-3. Seven phylogenetic trees of Paramyxoviruses were constructed from the entire and partial regions of P and V proteins.     

Cloning and sequence analysis of the hemagglutinin gene of the virulent strain of rinderpest virus

We have cloned the cDNA of the hemagglutinin (HA) gene of the virulent (Kabete O) strain of rinderpest virus and produced a comparative analysis of its sequence with that of the HA genes of rinderpest (lapinized strain) and measles viruses. The gene has an open reading frame of 1827 nucleotides, and the derived protein is 609 amino acids long with a calculated molecular weight of 68,006. The Kabete O HA polypeptide is identical in length to the HA of the lapinized strain of rinderpest virus and has a similar hydropathy profile. The nucleotide divergence between the lapinized and the Kabete O HA genes is 11.4% within the coding region, and 34.3% in the 3' untranslated region. The two rinderpest HA polypeptides differ at 74 amino acid residues for a divergence of 12.2%. Three-way comparison of the two rinderpest HA molecules with the measles virus HA polypeptide indicates that 56.6% of the residues are conserved.     

Sequence variation of the P gene among mumps virus strains

We have determined nucleotide sequences of a 183-nucleotide long region of the P gene of 10 mumps virus strains after gene amplification mediated by DNA polymerase catalyzed chain reaction (PCR) and have compared them with those of two strains which had been reported earlier (K. Takeuchi et al., J. Gen. Virol., 69, 2043-2049 (1988]. It was shown that mutation is generally noncumulative, i.e., most nucleotide substitutions in earlier strains do not appear in later strains. Viruses of different lineages appeared to cocirculate, but the comparison of American and Japanese strains suggested that those isolated in one country are more closely related to each other than to those isolated in the other country.     

Sequence analysis of the equine H7 influenza virus haemagglutinin gene.

The nucleotide sequences of ten haemagglutinin genes of representative H7N7 equine influenza viruses isolated between 1956 and 1977 have been determined by primer extension sequencing. Their nucleotide and deduced amino acid sequences demonstrate a high degree of homology. These equine viruses can be divided into two distinct subgroups, the prototype-like, and a group comprising the early American isolates and the remaining equine viruses. The equine H7 haemagglutinins form a quite distinct group compared to H7 haemagglutinins isolated from other species. Each of these equine H7 haemagglutinins possess a tetrabasic amino acid cleavage site separating the HA1 and HA2 domains but, in addition, all ten contain a nine amino acid insertion prior to the tetrabasic sequence. The haemagglutinin glycoproteins of all ten viruses are capable of cleavage activation in virus infected primary chicken embryo fibroblast cells.     

我国部分地区呼吸道合胞病毒地方株磷蛋白基因序列分析

目的 了解我国呼吸道合胞病毒（ＲＳＶ）地方株的Ｐ（Ｐｈｏｓｐｈｏｒｐｒｏｔｅｉｎ,Ｐ）蛋白基因状况和变异特征。方法 选取不同地区具有不同流行特征的６株ＲＳＶ地方株,以提取的病毒ｍＲＮＡ为模板进行逆转录－聚合酶链扩增（ＲＴ－ＰＣＲ）扩增、目的基因的克隆及序列测定分析。结果 地方株和同亚型原型株之间Ｐ蛋白核苷酸序列及推导出的氨基酸序列同源性均超过９５％;不同亚型间存在较大差异,核苷酸全序列同源性低于８５％,尤其在３′端非编码区及中间变异区。由氨基酸序列推导出的疏水性分析图显示,Ａ、Ｂ亚型中间变异区存在疏水性的不同,这为解释Ａ、Ｂ亚型间Ｐ蛋白电泳迁移率的不同提供了一种可能。结论 我国ＲＳＶ地方株与原型株之间的Ｐ蛋白无论在核苷酸水平还是在氨基酸水平均存在一定的变异。这些结果对于了解我国ＲＳＶ地方株的基因状况提供了有益的     

Sequence analysis of topoisomerase gene of pseudocowpox virus isolates from camels (Camelus dromedarius)

Topoisomerase gene of pseudocowposvirus from Indian dromedarian camel was amplified by PCR using the primers of PCPV from Finnish reindeer and cloned into pGEM-T for sequence analysis. Analysis of amino acid identity revealed that Indian PCPV of camel shared 95.9-96.8 with PCPV of reindeer, 96.2-96.5 with ORFV and 87.5 with BPSV.     

Molecular cloning of the rinderpest virus matrix gene: comparative sequence analysis with other paramyxoviruses

The nucleotide sequence of the gene encoding the matrix or membrane (M) protein of the virulent (Kabete-O) strain of rinderpest virus (RPV) has been determined. The M gene is 1457 nucleotides long with a single, large open reading frame. The derived polypeptide has 335 amino acids, corresponding to a calculated molecular weight of 38,289 and contains both small hydrophobic regions and many basic residues. The predicted amino acid sequence was compared to the M proteins of paramyxoviruses. Sequence comparison and hydropathy profiles among the morbilliviruses revealed that the M protein of RPV exhibits features similar to those of the M protein of MV and CDV. There is 78.2% homology at the amino acid level between the M protein of RPV and MV, and 77.6% between RPV and CDV. This indicates that a high degree of homology exists among the members of the genus Morbillivirus. In contrast, there is only 37.3 and 18% homology between RPV and bovine parainfluenza type 3 (BPV3), and RPV and Newcastle disease virus (NDV) M proteins, respectively. Thus the M proteins of the morbilliviruses are highly conserved whereas the M proteins of the genus Paramyxovirus show more divergence.     

Cloning of the fusion gene of rinderpest virus: comparative sequence analysis with other morbilliviruses

We have cloned the cDNA of the fusion (F) gene of the virulent (Kabete O) strain of rinderpest virus and provided a comparative analysis of its sequence with that of the F genes of measles and distemper viruses. The gene has an open reading frame of 2241 nucleotides with two potential initiation codons in-frame. Use of the first ATG would produce a polypeptide 747 amino acids long with a calculated molecular weight of 81,068. However, we suggest that the second ATG is used to generate the Fo protein, which is 546 amino acids long with a calculated molecular weight of 58,754. During maturation, the cleavage of F0 gives rise to the functional F1 and F2 polypeptides. The F1 polypeptide is 438 amino acids long and has a calculated molecular weight of 46,791, with a single (potential) glycosylation site in its cytoplasmic domain. The F2 polypeptide, probably 89 amino acids long after the signal sequence is cleaved, is estimated to be 9,800 Da and has three potential glycosylation sites. There is a divergence of 18.7% in amino acid sequences between rinderpest and measles virus F0 polypeptides; between distemper and rinderpest viruses the divergence is 31.8%. No significant homology in nucleotide sequences of rinderpest DNA to measles or distemper DNA was found in the 5' and 3' untranslated regions.     

Sequence analysis of the mumps virus mRNA encoding the P protein

The nucleotide sequence of the mumps virus phospho- or polymerase-associated (P) protein mRNA has been determined by sequencing a full-length cDNA clone and confirmed by partially sequencing the mRNA and the genome. The mRNA contains 1311 nucleotides excluding the poly(A) and encodes a protein of 390 amino acids with a calculated molecular weight of 41,574. Three small polypeptides were seen in in vitro translation of viral mRNA and hybrid-selected P mRNA, possibly representing internal initiation in the same reading frame of the P protein. A second overlapping reading frame is predicted from the sequence which has a capacity to code for two polypeptides of 56 and 34 amino acids, respectively. Whether these two polypeptides are expressed in infected cells is not known. Comparison of the P protein sequence with that of Sendai virus, measles virus, parainfluenza virus type 3, and canine distemper virus (CDV) showed no distinct homology but comparison with the P protein of Newcastle disease virus (NDV) showed 25.6% homology.     

Molecular characterization of Indian rabies virus isolates by partial sequencing of nucleoprotein (N) and phosphoprotein (P) genes

Rabies is endemic and an important zoonosis in India. There are very few reports available on molecular epidemiology of rabies virus of Indian origin. In this study to know the dynamics of rabies virus, a total of 41 rabies positive brain samples from dogs, cats, domestic animals, wildlife, and humans from 11 states were subjected to RT-PCR amplification of N gene between nucleotide N521-N1262 (742 bp) and P gene between nucleotide P239-P750 (512 bp). The N gene could be amplified from 30, while P gene from 41 samples, using specific sets of primers. The N gene-based phylogenetic analysis indicated that all Indian virus isolates are genetically closely related with a single cluster under arctic/arctic-like viruses. However, two distinct clusters were realized in P gene-based phylogeny viz., Rabies virus isolates of Punjab and Rabies virus isolates of remaining parts of India (other than Punjab). All the Indian rabies virus isolates were closely related to geography (>95% homology), but not to host species.     

Sequence analysis of the glucosyltransferase A gene (gtfA) from Streptococcus mutans Ingbritt.

The complete nucleotide sequence of a 2.4-kilobase fragment containing the glucosyltransferase A gene (gtfA) of Streptococcus mutans Ingbritt (serotype c) was determined. The gtfA gene contains 481 codons and specifies a protein of molecular weight 55,665. There is no evidence of a signal peptide in the protein or that the glucosyltransferase A enzyme is secreted. No sequence homologies were observed between the gtfA gene or protein and the gtfI or gtfB gene and its protein.     

人核糖体磷酸蛋白P2基因的克隆及鉴定

利用聚合酶链式反应技术（ＰＣＲ），从人肺巨细胞癌ＰＬＡ－８０１母系细胞系统克隆化高转移细胞株Ｄ中特异性扩增Ｐ２ ｃＤＮＡ（Ｈｕｍａｎ ｒｉｂｏｓｏｍａｌ ｐｈｏｓｐｈｏｐｒｏｔｅｉｎ Ｐ２ ｇｅｎｅ ｃＤＮＡ），并将扩增产物克隆入ｐＧＥＭ－３Ｚ载体，获得了重组质粒ｐＭＰ２，对其中两个克隆ｐＭＰ２－１、ｐＭＰ２－２的Ｐ２ ｃＤＮＡ进行了序列分析。结果表明：ｐＭＰ２－１的Ｐ２ｃＤＮＡ序列与文献报道基本     

Sequence analysis of the RNA polymerase gene of African horse sickness virus

Summary.  The gene encoding the inner core protein VP1 of African horse sickness virus (AHSV) serotype 9 has been cloned, expressed in vitro and entirely sequenced, completing molecular characterization of the AHSV genome. An analysis of the sequence supporting the identity of AHSV VP1 as the putative viral RNA polymerase is presented. Accepted August 24, 1997 Received July 28, 1997