Nucleotide sequence of the gene encoding the matrix protein of mumps virus (Miyahara strain)

The nucleotide sequence of the gene encoding the matrix (M) protein of mumps virus (MuV), Miyahara strain, has been determined from several overlapping cDNA clones. The M protein mRNA is 1248 nucleotides in length, exclusive of the poly(A) tail, and codes for a protein of 375 amino acids (Mr41,556). Comparison of the deduced amino acid sequence of the M protein of the Miyahara strain with that of the SBL-1 strain revealed that the M proteins of both strains are highly conserved. A significantly lower rate of nucleotide differences conducive to amino acid differences in the M gene compared with other genes appeared to indicate the importance of the conserved primary structure of the M protein for its function.Requests for reprints should be addressed to Kiyoshi Tanabayashi, Department of Measles Virus, National Institute of Health, 4-7-1 Gakuen, Musashimurayama, Tokyo 190-12, Japan.     

Complete sequence of a subgroup 3.4 strain of classical swine fever virus from Taiwan

Classical swine fever viruses from Taiwan have been classified into two subgroups (3.4 and 2.1). Outbreaks caused by 3.4 viruses were reported in Taiwan prior to 1996 and which mainly distributed in the geographic range from southern Japan to Taiwan. We have determined the complete sequence of a reference strain, 94.4/IL/94/TWN. The genome contains 12,296 nucleotides, encoding 3,898 amino acids flanked by a 372-nt region at the 5' untranslated region (UTR) and a 227-nt region at the 3'-UTR. Similarities of nucleotides among 3.4 viruses isolated from Taiwan and Japan (Kanagawa/74; Okinawa/86) maintained in 94.2-97.5%; however, comparing to subgroup 1.1 (ALD/64/Jap) and 2.1 (TD/96/TWN) only showed about 72.5-80.8%, respectively. Phylogenetic analysis based on positioning from 11,157 to 11,565 nt (NS5B region) revealed that CSFVs were divided into three major lineages and their sublineages. Strain 94.4/IL/94/TWN is the first completely genomic sequence of subgroup 3.4 viruses.     

A persistent infection of baby hamster kidney-21 cells with mumps virus and the role of temperature-sensitive variants.

A persistent infection of baby hamster kidney-21 (BHK-21) cells with mumps virus (BHKpi) was maintained for over 60 cell passages in the absence of antiserum. Viral persistence was demonstrated in the cultures by hemadsorption, immunofluorescence, multinucleate syncytia, and released mumps virus at the level of 10(2)--10(3) fluorescent focus-forming units/ml. No detectable levels of interferon were found in cultures persistently infected with mumps virus. Approximately 85--95% of the cells contained viral antigens. Nuclear fluorescence was observed in the persistently infected cells. Mumps virus from persistently infected clutures (MuVpi) was more heat-labile than wild-type mumps (MuVo) when subjected to 40 degrees C. BHKpi cells had a more rapid doubling time and a higher cloning efficiency in soft agar in comparison to BHK-21 cells. MuVpi was also found to be temperature-sensitive. The temperature-sensitivity of MuVpi was determined by the efficiency of plating at 33 degrees and 39 degrees C. MuVpi readily established a persistent infection in BHK-21 cells with less cytopathology than MuVo, and released temperature-sensitive virus.     

Changes in mumps virus neurovirulence phenotype associated with quasispecies heterogeneity

Mumps virus is a highly neurotropic virus with evidence of central nervous system invasion (CNS) in approximately half of all cases of infection. In countries where live attenuated mumps virus vaccines were introduced, the number of mumps cases declined dramatically; however, recently, the safety of some vaccine strains has been questioned. For example, one of the most widely used vaccines, the Urabe AM9 strain, was causally associated with meningitis, leading to the withdrawal of this product from the market in several countries. This highlights the need for a better understanding of the attenuation process and the identification of markers of attenuation. To this end, we further attenuated the Urabe AM9 strain by serial passage in cell culture and compared the complete nucleotide sequences of the parental and passaged viruses. Interestingly, despite a dramatic decrease in virus virulence (as assayed in rats), the only genomic changes were in the form of changes in the level of genetic heterogeneity at specific genome sites, i.e., either selection of one nucleotide variant at positions where the starting material exhibited nucleotide heterogeneity or the evolution of an additional nucleotide to create a heterogenic site. This finding suggests that changes in the level of genetic heterogeneity at specific genome sites can have profound neurovirulence phenotypic consequences and, therefore, caution should be exercised when evaluating genetic markers of virulence or attenuation based only on a consensus sequence.     

Characterisation of mumps virus genotype C among patients with mumps in India

Measles, mumps and rubella (MMR) vaccine failure had been reported globally and here, we report that it occurs in India now. MMR vaccinated people have developed acute mumps accompanied by anti-mumps immunoglobulin M. Genotypic characterisation revealed that the circulating mumps strain was genotype C, which is distinct from the vaccine strain of genotype N (L-Zagreb). This is the first report in India to suggest that genotype C is responsible for the present mumps infection. Thus, the present MMR vaccine must be revamped and optimised for its efficacy to prevent any future mumps epidemics.     

Hemagglutinin-neuraminidase sequence and phylogenetic analyses of mumps virus isolates from a vaccinated population in Singapore

During 1999-2000, a sustained mumps outbreak in the highly vaccinated population in Singapore was attributed to vaccine failure associated with the Rubini vaccine strain. To explain this phenomenon, the complete nucleotide and amino acid sequences of the hemagglutinin-neuraminidase (HN) gene of eight mumps virus isolates from patients with parotitis in Singapore were determined and compared with those of known vaccine strains. Phylogenetic trees constructed on the basis of HN nucleotide and amino acid sequences showed that the Singapore mumps virus isolates were more closely related to the Urabe strain and belonged to a different cluster from the Rubini and Jeryl-Lynn strains. The Rubini vaccine showed only approximately 93% nucleotide and approximately 96% amino acid sequence similarity to Urabe and Singapore isolates. Compared with the vaccine strains, six of the eight isolates lacked the extracellular glycosylation site at residues 400-402. Other significant amino acid disparities (e.g., at residue 354) may also affect the antigenic properties of the HN protein. These findings suggest that the evolution and adaptation of the currently circulating mumps virus strains in the community has led to the emergence of genetically distinct viral strains. The low vaccine efficacy of the Rubini strain represents a major reason for the recent mumps resurgence and failure of mumps immunization in Singapore.     

Identification of a new genotype H wild-type mumps virus strain and its molecular relatedness to other virulent and attenuated strains

A single clinical isolate of mumps virus designated 88-1961 was obtained from a patient hospitalized with a clinical history of upper respiratory tract infection, parotitis, severe headache, fever and lymphadenopathy. We have sequenced the full-length genome of 88-1961 and compared it against all available full-length sequences of mumps virus. Based upon its nucleotide sequence of the SH gene 88-1961 was identified as a genotype H mumps strain. The overall extent of nucleotide and amino acid differences between each individual gene and protein of 88-1961 and the full-length mumps samples showed that the missense to silent ratios were unevenly distributed. Upon evaluation of the consensus sequence of 88-1961, four positions were found to be clearly heterogeneous at the nucleotide level (NP 315C/T, NP 318C/T, F 271A/C, and HN 855C/T). Sequence analysis revealed that the amino acid sequences for the NP, M, and the L protein were the most conserved, whereas the SH protein exhibited the highest variability among the compared mumps genotypes A, B, and G. No identifying molecular patterns in the non-coding (intergenic) or coding regions of 88-1961 were found when we compared it against relatively virulent (Urabe AM9 B, Glouc1/UK96, 87-1004 and 87-1005) and non-virulent mumps strains (Jeryl Lynn and all Urabe Am9 A substrains).     

Rescue of wild-type mumps virus from a strain associated with recent outbreaks helps to define the role of the SH ORF in the pathogenesis of mumps virus

Mumps virus (MuV) causes acute infections in humans. In recent years, MuV has caused epidemics among highly vaccinated populations. The largest outbreak in the U.S. in the past 20 years occurred in 2005-2006 with over 5000 reported cases in which the majority of the cases was in vaccinated young adults. We sequenced the complete genome of a representative strain from the epidemic (MuV-IA). MuV-IA is a member of genotype G, the same genotype of MuV that was associated with the outbreak in the UK in 2004-2005. We constructed a reverse genetics system for MuV-IA (rMuV-IA), and rescued a virus lacking the open reading frame (ORF) of the SH gene (rMuV?SH). rMuV?SH infection in L929 cells induced increased NF-κB activation, TNF-α production and apoptosis compared to rMuV-IA. rMuV?SH was attenuated in an animal model. These results indicated that the SH ORF of MuV plays a significant role in interfering with TNF-α signaling and viral pathogenesis during virus infection.     

Comparative studies of five strains of mumps virus in vitro and in neonatal hamsters: evaluation of growth,cytopathogenicity, and neurovirulence

The growth and Cytopathogenicity of five strains of mumps virus were examined in six types of cell cultures and in neonatal hamsters. These strains included the MJ and RW strains, both recent cerebrospinal fluid isolates; the neuroadapted Kilham strain; the Enders strain adapted to chick embryo; and the Jeryl Lynn vaccine strain adapted to chick cell culture. The MJ, RW, and Kilham strains all produced infectious virus without restriction in vitro, but the RW strain did not cause obvious cytopathic effect; the MJ and Kilham strains were cytopathic. The Enders and Jeryl Lynn strains adapted to chick embryo cells were cytopathic and productive in chick cell culture but were restricted in ability to grow productively in vitro on mammalian cell types, even failing to produce noninfectious particles in some cases. In vitro Cytopathogenicity was a host-independent property of a specific virus strain, but the type of cytopathic effect manifest in culture (eg, fusion, cytoplasmic vacuoles) depended on both the strain and the host cell. The ability of a virus strain to invade the brain parenchyma and infect neurons in vivo appeared to correlate with the strain's Cytopathogenicity and not with passage history or adaptive status.     

Complete genomic sequence and phylogenetic relatedness of hepatitis B virus isolates in Cambodia

Although it is known that Cambodia is one of the high endemic area of hepatitis B virus (HBV) infection, molecular characterization of HBV circulating in this country has not been reported. In this study, pre-S gene of HBV from 12 Cambodian patients was sequenced. Phylogenetic analysis based on the pre-S gene sequence revealed that 8 out of 12 isolates (66.7%) belonged to HBV/C1 and remaining four (33.3%) were HBV/B4. Furthermore, complete genomic sequences were also determined for three Cambodian HBV isolates. They all comprised of 3,215 bp long and two of them belonged to subgenotype B4, which had recombination event with genotype C in the precore/core gene confirmed by SimPlot and BootScanning analyses. Our results showed that both HBV strains belonged to subgenotypes B4 and C1, which are circulating in this country. This is the first report on molecular characterization of the HBV prevalent in Cambodia.     

Local production of mumps IgG and IgM antibodies in the cerebrospinal fluid of meningitis patients

Immunoglobulin G (IgG) and M (IgM) antibodies against mumps virus were measured by an enzyme-linked immunosorbent assay (ELISA) in the serum and cerebrospinal fluid (CSF) specimens of patients with mumps meningitis. The CSF IgG antibodies correlated well with the respective antibody titers in serum. On the contrary, in only about half of the patients a moderate correlation was found between the CSF and serum IgM antibody titers, while the other patients did not have detectable mumps IgM antibodies in CSF irrespective of intermediate to high titers in serum. Two different immunologic mechanisms may be involved in these two groups which, however, did not show any clinical differences. The lack of IgM antibodies in the CSF of many patients diminished the value of CSF in the laboratory diagnosis of mumps meningitis compared to use of serum specimens. Intrathecal synthesis of mumps IgG antibodies was demonstrated in 83% of the patients, and of IgM antibodies in at least 67% of those patients with detectable IgM antibodies in CSF. The ratio between mumps IgG and IgM antibodies was higher in CSF than in serum, suggesting that the synthesis of IgG antibodies in central nervous system was more efficient than that of IgM antibodies.     

流行性腮腺炎疫苗株S79全基因序列测定与分析

目的 腮腺炎疫苗株S79工作种子噬斑纯化及全基因组测序,针对国内已经分离出的毒株,从分子生物学角度探讨疫苗保护力相关问题.方法 噬斑纯化S79疫苗株,利用RT-PCR分段扩增S79株两种亚株的全基因并测序,比较S79株与其来源株Jeryl Lynn(JL)核酸序列差异;从GenBank中获得WHO各基因型参考株和中国腮腺炎流行株疏水蛋白(SH)序列,分析病毒株和疫苗株遗传距离,并构建基因亲缘性关系树.结果 S79疫苗株由两种亚株构成,比例为2∶5(major∶minor),获得全基因序列并递交GenBank;与相应的JL株相比,核苷酸序列同源性分别为99.7%和100%.亚株序列中存在散在区段异源重组.S79疫苗株为A基因型,中国的流行株为F基因型,遗传距离为11.2%～20.0%.结论 S79疫苗株由两种亚株构成,两亚株的全基因序列与JL株基本一致,但亚株的比例与国际上应用的其他JL疫苗株存在较大差异.疫苗株与中国流行株不属于同一基因型,遗传距离较远.S79疫苗免疫保护效果的差异可能主要与疫苗株和流行株不属于同一基因型有关.     

Hepatitis E virus genotyping based on full-length genome and partial genomic regions

Some genomic regions for hepatitis E virus (HEV) genotyping have been reported to correlate well with the results from the phylogenetic analyses on the basis of the complete genome. However, few studies have systemically investigated the genomic regions for HEV genotyping using a combined phylogenetic and statistical approach. A consensus region for HEV genotyping has not been determined. In this study the nucleotide identities and genetic distances of 24 partial genomic regions and the complete genome sequences of 37 HEV strains were compared statistically. It was demonstrated with both one-way ANOVA and two-way ANOVA that only one genomic region in RNA-dependent RNA polymerase domain (4254–4560 nt) for which there were no significant differences when compared with the full-length genome (P > 0.05). The same four genotypes were identified by phylogenetic analysis based on this statistically predicted region identified as for the complete genome. RT-PCR amplification of HEV strains from all four genotypes confirmed conservation of the flanking primer sites of this region. Serum samples from 20 patients with a clinical diagnosis of hepatitis E were further analyzed by PCR using the same primers, 13 were positive and could be classified into genotype 4. These data strongly suggested that this newly identified region could be used for future HEV genotyping.     

Molecular cloning and complete nucleotide sequence of genomic RNA of the AIK-C strain of attenuated measles virus

Twelve cDNA clones covering the entire genome of the AIK-C strain of a seed for live measles vaccine were obtained, and the nucleotide sequences were determined. The full viral genomic RNA consists of 15,894 nucleotides. Comparisons of the nucleotide sequence and the deduced amino acid sequence between the AIK-C and other Edmonston strains revealed the following changes: 56 nucleotide differences and one C residue insertion, 31 amino acid changes, and 19 silent mutations.     

Mapping antigenic diversity and strain specificity of mumps virus: a bioinformatics approach

Mumps is an acute infectious disease caused by mumps virus, a member of the family Paramyxoviridae. With the implementation of vaccination programs, mumps infection is under control. However, due to resurgence of mumps epidemics, there is a renewed interest in understanding the antigenic diversity of mumps virus. Hemagglutinin-neuraminidase (HN) is the major surface antigen and is known to elicit neutralizing antibodies. Mutational analysis of HN of wild-type and vaccine strains revealed that the hypervariable positions are distributed over the entire length with no detectable pattern. In the absence of experimentally derived 3D structure data, the structure of HN protein of mumps virus was predicted using homology modeling. Mutations mapped on the predicted structures were found to cluster on one of the surfaces. A predicted conformational epitope encompasses experimentally characterized epitopes suggesting that it is a major site for neutralization. These analyses provide rationale for strain specificity, antigenic diversity and varying efficacy of mumps vaccines.     

新分离登革2型病毒福建株基因组全序列的测定

目的 对新近分离的导致1999年福建省登热流行的登革2型病毒FJ－10株进行基因组全序列测定及系统发生树分析。方法 利用RT－PCR和5′、3′RACE法扩增FJ－10株cDNA,并进行克隆测序,利用DNASTAR折Clustal方法绘制系统发生树。结果 JF－10株基因组全长10723个核苷酸,有1个单一开放读码框架（ORF,第97－10269nt）,编码3391个氨基酸,5′和3′非编码区长度分别为96和454个核苷酸,通过与标准株NGC株和我国其他地区分离株DEN2－04、43、44株比较,核苷酸同源性分别为94.0%、92.8%、93.9%和93.9%,氨基酸同源性分别为97.9%、97.2%、97.7%和97.9%。以47株登革2型病毒E／NS1连接区240个核苷酸序列进行发生树分析,福建株与印度尼西亚和斯里兰卡分离株亲缘关系较近,同属第Ⅳ基因型。结论 FJ－10株基因组全序列一级结构与其他登革2型病毒类似,其基因型不同于我国其他地区分离株DEN2－04、43和44株。