Molecular cloning and sequence analysis of the rinderpest virus mRNA encoding the hemagglutinin protein

Genetic characterization of the Korean LATC06 rinderpest vaccine strain

We sequenced the genome of LATC06 generated by in vitro passage in Vero cells of the lapinized-avianized (LA) strain and compared its sequence to those of other rinderpest viruses. The LATC06 genome consists of 15882 nucleotides. Its transcriptional regulatory control sequences (TRSs) at gene boundaries are identical to those of the Kabete O strain. Cleavage sites for generating F1/F2 proteins were identified in the same amino acid position (aa 108) as F proteins in LATC06, L13, RBT1, Kabete O, and RBOK strains. There are three predicted N-glycosylation sites of H proteins in LA (Japan) and LATC06 strains. The six epitopes of H protein in the LA (Japan) strain that elicit immunodominant humoral responses are also found in the LATC06 strain.

Sequence and phylogenetic analyses of the structural genes of virulent isolates and vaccine strains of peste des petits ruminants virus from India

Peste des petits ruminants (PPR) is an acute, highly contagious, notifiable and economically important transboundary viral disease of sheep and goats. In this study, sequence and phylogenetic analyses of structural protein genes, namely the nucleocapsid (N), the matrix (M), the fusion (F) and the haemagglutinin (H) coding sequences of virulent and vaccine strains of PPR virus (PPRV), were undertaken to determine the genetic variations between field isolates and vaccine strains. The open reading frame (ORF) of these genes of the isolates/strains was amplified by RT-PCR, cloned and sequenced. The ORF of N, M, F and H genes was 1578, 1008, 1641 and 1830 nucleotides (nt) in length and encodes polypeptides of 525, 335, 546 and 609 amino acids (aa), respectively, as reported earlier. Comparative sequence analyses of these four genes of isolates/strains were carried out with published sequences. It revealed an identity of 97.7-100% and 97.7-99.8% among the Asian lineage IV and 89.6-98.7% and 89.8-98.9% with other lineages of PPRV at nt and aa levels, respectively. The phylogenetic analyses of these isolates based on the aa sequences showed that all the viruses belonged to lineage IV along with other Asian isolates. This is in agreement with earlier observations that only PPRV lineage IV is in circulation in India since the disease was first reported. Further, sequence analysis of the thermostable/thermo-adapted vaccine strains showed no significant changes in the functional or structural surface protein-coding gene sequences. It is important to monitor the circulation of the PPRV in susceptible animals by H gene-based sequence comparisons in addition to the F gene- and N gene-based approaches to identify the distribution and spread of virus in the regular outbreaks that occur in endemic countries like India.

Pathological and phylogenetic features of prevalent canine distemper viruses in wild masked palm civets in Japan

Ten wild masked palm civets infected with canine distemper virus (CDV), captured in Japan from 2005 to 2007, were histopathologically and phylogenetically analyzed. Phylogenetic analysis based on the amino acid sequences of the H protein of two CDV isolates from masked palm civets revealed that the two isolates were classified into the clade of recent isolates in Japan. Histopathologically marked lesions of virus encephalitis were present in the brain, whereas gastrointestinal lesions were absent or at a mild degree. The distribution of the lesions resembles that of recent CDV cases in dogs. Therefore, recent CDV infections in masked palm civets could be caused by recently prevalent CDV in dogs. The possibility of the masked palm civet as a spreader of CDV among wildlife is also discussed.

Sequence analysis of the haemagglutinin and fusion protein genes of peste-des-petits ruminants vaccine virus of Indian origin

The amino acid composition of the two surface proteins of peste-des-petits ruminants vaccine virus belonging to lineage four from India were deduced from the nucleotide sequence. The fusion (F) protein gene of PPRV Sungri/96 is 2405 nucleotides long and in relation to the length, it is 80 nucleotides longer than that of PPRV Nigeria/75/1 which are found to be present at the 5'UTR of this virus. The complete F gene alignment with other morbillivirus reveals a homology of 89% with PPRV/Nigeria/75/1 and 48-51% with other morbilliviruses. The F protein of PPRV Sungri/96 exhibited characteristics similarity to those of other morbillivirus F proteins. The overall amino acid similarity with its counterpart PPRV Nigeria/75/1 was 96%; with other morbilliviruses it is 65-74%. The PPRV Sungri/96 haemagglutinin (H) protein gene is 1954 nucleotides long and showed a sequence homology of 90.7% with PPRV/Nigeria/75/1 and with other morbilliviruses it ranged from 33% to 45%. At amino acids level, PPRV Sungri/96 showed a homology of 92.3% with PPRV/Nigeria/75/1 and 34-49% with other morbilliviruses. The phylogenetic tree constructed for F and H gene reveals four separate groups which is very similar to that found in other genes. To the best of our knowledge this is the first report describing the F and H genes of an Indian isolate.

Phylogenetic analysis of the hemagglutinin (H) gene of canine distemper viruses isolated from wild masked palm civets (Paguma larvata)

Hemagglutinin (H) gene of two CDV isolates, the Haku93 and Haku00 strains, from masked palm civets was molecularly analyzed. H genes of both two CDVs contained one open reading frame encoding 607 amino acids. Nucleotide and predicted amino acid sequences of H gene of the CDV Haku93 and Haku00 revealed high similarity to those of recent field isolates such as the Yanaka and Tanu96, while they showed limited identity to those of old vaccine strains. Potential N-linked glycosylation sites in both Haku93 and Haku00 were identical to other recent CDV isolates. Phylogenetic analysis revealed that the CDV strains derived from masked palm civets were classified into the group of recent Japanese CDV isolates.

Mapping of T-helper epitopes of Rinderpest virus hemagglutinin protein

Rinderpest virus (RPV) is a highly contagious and often fatal disease of domestic and wild ruminants, caused by rinderpest virus of the genus Morbillivirus under the family Paramyxoviridae. Hemagglutinin (H) and fusion (F) proteins of this enveloped virus confer protective immunity against experimental challenge with virulent rinderpest virus. We have earlier demonstrated that immunization with a single dose of recombinant extracellular baculovirus expressing H protein elicits H-specific humoral and lymphoproliferative responses in cattle. The lymphoproliferative responses are predominantly BoLA class II restricted. In this work, we have analyzed lymphoproliferative responses of peripheral lymphocytes from immunized cattle to truncated H protein fragments expressed in E. coli for locating domains harboring Th epitopes. One region (aa 113-182) recognized by immune T cells is conserved in the H protein of measles virus, which was earlier shown to contain a dominant Th epitope in mouse. Synthetic peptides within this region of measles virus H protein were used to identify a Th epitope conserved in the H protein of RPV virus (aa 123-137) in cattle. A second Th epitope located at the C-terminus of RPV-H was mapped to the region corresponding to aa 512-609 using truncated protein fragments expressed in E. coli. The C-terminal epitope (aa 575-583) was mapped using synthetic peptides corresponding to measles virus H as well as RPV-H protein.

Cytoplasmic domain of Sendai virus HN protein contains a specific sequence required for its incorporation into virions

In the assembly of paramyxoviruses, interactions between viral proteins are presumed to be specific. The focus of this study is to elucidate the protein-protein interactions during the final stage of viral assembly that result in the incorporation of the viral envelope proteins into virions. To this end, we examined the specificity of HN incorporation into progeny virions by transiently transfecting HN cDNA genes into Sendai virus (SV)-infected cells. SV HN expressed from cDNA was efficiently incorporated into progeny Sendai virions, whereas Newcastle disease virus (NDV) HN was not. This observation supports the theory of a selective mechanism for HN incorporation. To identify the region on HN responsible for the selective incorporation, we constructed chimeric SV and NDV HN cDNAs and evaluated the incorporation of expressed proteins into progeny virions. Chimera HN that contained the SV cytoplasmic domain fused to the transmembrane and external domains of the NDV HN was incorporated to SV particles, indicating that amino acids in the cytoplasmic domain are responsible for the observed specificity. Additional experiments using the chimeric HNs showed that 14 N-terminal amino acids are sufficient for the specificity. Further analysis identified five consecutive amino acids (residues 10 to 14) that were required for the specific incorporation of HN into SV. These residues are conserved among all strains of SV as well as those of its counterpart, human parainfluenza virus type 1. These results suggest that this region near the N terminus of HN interacts with another viral protein(s) to lead to the specific incorporation of HN into progeny virions.

Construction of recombinant vaccinia virus expressing Rinderpest Virus nucleocapsid protein and its immunogenicity in mice

Recombinant vaccinia virus (rVV) was constructed by inserting Rinderpest Virus (RPV) nucleocapsid (N) protein gene. The rVV expressed RPV-N protein in the rVV-infected cells. The rVV was shown to produce RPV-N-specific antibody in mice.

The transmembrane domain in viral fusion: essential role for a conserved glycine residue in vesicular stomatitis virus G protein

The transmembrane (TM) domains of viral fusion proteins are required for fusion, but their precise role is unknown. G protein, the fusion protein of vesicular stomatitis virus, was previously shown to lose syncytia-forming ability if six residues (GLIIGL) were deleted from its TM domain. The 20-residue TM domain of wild-type (TM20) G protein was thus changed into a TM domain of 14 residues (TM14). To assess possible sequence specificity for this loss of function, the two Gly residues in TM20 were replaced with either Ala or Leu. Both mutations resulted in complete loss of fusion activity, as measured by fusion-dependent reporter gene transfer. Single substitutions decreased activity by about half. TM14 was weakly active (15%) but reintroduction of a Gly residue into TM14 by a single Ile --> Gly substitution increased activity to 80%. All mutants retained normal hemifusion activity, i.e., lipid mixing between the outer leaflets of the reacting membranes. Thus, at least one TM Gly residue is required for a late step in fusion mediated by G protein. Gly residues were significantly (2.6-fold; P = 0.004) more abundant in the TM domains of viral fusion proteins than in those of nonfusion proteins and were distributed differently within the TM domain. Thus, Gly residues in the TM domain of other viral fusion proteins may also prove to be important for fusion activity.

Characterization of membrane-bound and membrane anchor-less forms of hemagglutinin glycoprotein of Rinderpest virus expressed by baculovirus recombinants

The Rinderpest virus (RPV) hemagglutinin (H) is a class 2 glycoprotein by means of which the virus attaches to the host cell receptor. A full length cDNA coding for H protein was used to construct a recombinant baculovirus expressing the H protein, recH(M), on the surface of insect cells. The small N terminal cytoplasmic domain was deleted and the transmembrane domain which extends from amino acids 35 to 59 was replaced with a signal peptide derived from the ecdysteroid UDP glycosyl transferase (egt) gene of the baculovirus, AcNPV. The protein recH(sec) expressed by the recombinant baculovirus carrying this engineered gene was secreted into the medium. Both forms of recombinant H protein retained reactivity with conformation-dependent monoclonal antibodies. The recH(M) was recognized by antibodies made in cattle either as the result of vaccination or natural infection. The soluble form of H is a valuable tool for studying the structure and function of the RPV H glycoprotein.

Genetic variability of the glycoprotein genes of current wild-type measles isolates

The glycoprotein coding sequences from three wild-type measles viruses isolated in the United States during 1988-1989 were examined by mRNA templated sequencing to determine whether contemporary strains have undergone genetic changes relative to the vaccine strain, Moraten. These studies revealed variation in the hemagglutinin (HA) gene and, to a far lesser degree, the fusion (F) gene. The F protein coding region was highly conserved with only three predicted amino acid changes. Among the predicted amino acid changes identified in the HA was a new potential glycosylation site at residue 416, located toward the carboxy-terminal end of the HA peptide. Eighty percent of the predicted amino acid changes in the HA shared by the three wild-type isolates were clustered near the five previously identified potential glycosylation sites. A linear pattern of evolutionary change was observed after comparing the predicted amino acid HA changes from the 1988-1989 viruses to those predicted in the HA protein from U.S. wild types isolated in 1977 and 1983.

The nucleotide and predicted amino acid sequence of the attachment protein of canine distemper virus

The nucleotide sequence of the gene coding for the attachment protein of the Convac strain of the canine distemper virus (CDV), corresponding to the haemagglutinin (H) gene of measles virus was determined using a mRNA-derived cDNA clone and genomic viral RNA. The mRNA transcribed from the CDV H gene is 1944 nucleotides long excluding the polyadenylated tail. Only one long open reading frame was found comprising nucleotides 21-1841. The predicted protein has a single hydrophobic region which can serve as a membrane anchoring domain. The deduced 607 amino acids would code for a protein of 68,247 Da, to be compared with an approximate protein molecular weight in SDS-PAGE of the glycosylated protein, which is 85,000 Da. The CDV H protein exhibited seven potential N-linked glycosylation sites. These were concentrated to the carboxyterminal part of the CDV H protein and differed markedly from measles virus (MV) and rinderpest virus (RPV) where the potential sites were mostly conserved and located in the amino-terminal half of the proteins. In spite of the differences in amino acid composition of these three H proteins their hydrophilicity/hydrophobicity plots were closely similar with the major hydrophobic region at an identical location. All the 12 cysteine residues found in the CDV H protein were conserved in MV and RPV. The amino acid homology between CDV and MV H protein was 37% and between CDV and RPV H protein 38%. The fact that the corresponding homology between the MV and RPV proteins is almost 60% shows that the evolutionary separation between CDV and RPV occurred at a much earlier time than the separation between RPV and MV.

Nucleotide sequence of cDNA to the rinderpest virus mRNA encoding the nucleocapsid protein

The full-length cDNA corresponding to the mRNA encoding the nucleocapsid protein (NP) of rinderpest virus (RV) was cloned and its complete nucleotide sequence was determined. The gene of RV-NP was composed of 1683 nucleotides and contained a single large open reading frame, which is capable of encoding a protein of 525 amino acids with a molecular weight of 58,241 Da. The nucleotide sequence and predicted amino acid sequence were compared with those of measles virus (MV) and canine distemper virus (CDV). The nucleotide sequence of the coding region of RV-NP (53-1630) revealed a homology of 68.1% and 63.0% with MV and CDV-NP, respectively. Relatively moderate homologies of 68.7% (MV) and 64.3% (CDV) were found at nucleotides 53-592. The highest homology of 75.3-74.3% was equally present between RV and both MV and CDV in the middle region at nucleotides 593-1312. The homologies of the predicted amino acids in this region were 88.3% (MV) and 86.3% (CDV). Relatively low (MV) or little (CDV) homology was detected in the last 318 nucleotides toward the 3' terminus (1313-1630). The predicted secondary structures of amino acids at the C terminus differed between the three viruses.

Morbillivirus group: genome organisation and proteins

The Paramyxoviridae family is divided into three genera: Paramyxovirus, Pneumovirus and Morbillivirus. In the last group, there are four closely related viruses which are seriously pathogenic for man and animals, and usually cause acute diseases. At least two of them (measles and canine distemper viruses) can cause a persistent infection which leads to a chronic disease of the nervous system that, in the end, is fatal. For a long time, the biochemical analysis of morbilliviruses was hampered by the high susceptibility of some of their proteins to proteolysis. With cloning and sequencing technology, more data on the biology of those viruses are now available.

Development of heat-stable recombinant rinderpest vaccine

Recombinant vaccinia virus (RVV) containing the full-length cDNA of rinderpest virus (RV)-haemagglutinin (H) gene was constructed. The H gene was inserted into the attenuated vaccine strain of vaccinia virus (VV), Le 16 m0, with two different promoters, namely cowpox virus A-type inclusion body (ATI) promoter or VV 7.5 kilodalton (P7.5) promoter. These RVVs produced the same sized fully glycosylated RV-H protein in RK 13 cells as that of the authentic RV-H. Their heat stability in the lyophylized state was similar to that of the parental VV. All rabbits immunized with these RVVs produced virus neutralizing (VN) antibody to RV as well as anti RV-H antibody. Four weeks after immunization, these animals were challenged with RV intravenously. None of the RVV-immunized rabbits developed any clinical signs of RV infection except one which was immunized with RVV containing the ATI promoter and developed low VN titer. These results indicate the possibility of developing a heat-stable recombinant vaccine for the eradication of rinderpest in tropical countries without cold storage systems.

Natural infection with canine distemper virus in a Japanese monkey (Macaca fuscata)

A case of encephalitis in a Japanese monkey (Macaca fuscata) was examined histopathologically and serologically. The animal had brain lesions consisting of perivascular cuffs, malacia, inclusion bodies and giant cells. Monoclonal antibody to the nucleoprotein of canine distemper virus (CDV) stained the inclusions, and the distribution of the virus antigen was closely associated with that of the histological lesions. Serologically, all the 22 monkeys in the same group as the diseased monkey had relatively high titers of neutralizing antibody to CDV, but not to measles virus (MV). The pattern of the antibody titers to CDV and MV closely resembled that of cynomolgus monkeys experimentally inoculated with CDV, but differed from that of monkeys inoculated with MV. These findings suggest that an epidemic of CDV occurred in these Japanese monkeys, associated with one case of fatal viral encephalitis. This is believed to be the first report of a natural infection by CDV in non-human primates.

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.

Fusion glycoprotein (F) of rinderpest virus: entire nucleotide sequence of the F mRNA, and several features of the F protein

The full-length cDNA corresponding to the mRNA for the fusion protein of rinderpest virus (RV) was cloned and its complete nucleotide sequence was determined. The mRNA for the F protein was composed of 2359 nucleotides and contained a single large open reading frame which was capable of encoding 566 amino acids with a molecular weight (MW) of 58,929. The RV-F mRNA had a long noncoding region at the 5' end (586 bases) which was C-rich like the measles virus (MV)-F mRNA but they did not appear to be homologous with each other. Their secondary structure with long G-C stems suggested that they are easily folded. The coding region of RV-F mRNA was significantly homologous with that of MV-F; 74% of the nucleotides and 79.0% [corrected] of the amino acids were identical. The predicted RV-F protein had a basic amino acid region (104-108) which may be cleaved by protease to yield an activated form of F1,2. Three regions (1-19, 109-133, 418-513) were highly hydrophobic, and the N-terminal hydrophobic region of F1 or the positions of cysteines were significantly conserved compared with those of the other paramyxovirus F proteins. Three potential sites for glycosylation existed only in the F2 protein. Several features of the predicted RV-F protein were confirmed in polyacrylamide gel electrophoresis.

Structure, function, and intracellular processing of paramyxovirus membrane proteins

Paramyxoviruses are a fascinating group of viruses with diverse hosts and disease manifestations. They are valuable systems for studying viral pathogenesis, molecular mechanisms of negative strand viral replication, and glycoprotein structure and function. In the past few years this group of viruses has received increased attention and as a result there is a wealth of new information. For example, most of the genes of many paramyxoviruses have been cloned and sequenced. The recent availability of sequence information from a number of paramyxoviruses now allows the direct comparison of the amino acid sequence and determinants of secondary structure of analogous genes across the family of viruses. Such comparisons are revealing for two reasons. First, results provide clues to the evolution of these viruses. Second, and more importantly, comparisons of analogous genes may point to sequences and structural determinants that are central to the function of the individual proteins. Below is a comparison of five of the paramyxovirus genes with a discussion of the implications of common structural determinants for function, intracellular processing, and evolutionary origin. The focus is on the paramyxovirus membrane proteins, although other proteins are discussed briefly.