Molecular cloning and nucleotide sequence of the pestivirus bovine viral diarrhea virus

The RNA genome of the cytopathic NADL isolate of bovine viral diarrhea virus (BVDV) has been molecularly cloned and the nucleotide sequence determined. The cloned sequence was 12,573 nucleotides in length, corresponding to a molecular weight of 4.3 X 10(6), having a base composition of 32.2% A, 25.7% G, 22.1% U, and 20.0% C. However, the sequences at the 5' and 3' termini of the RNA have not been unequivocally established. A single major open reading frame extending the length of the molecule was found in the viral-sense (positive polarity) sequence. This open reading frame was capable of encoding 3988 amino acids, representing 449 kDa of protein.     

Molecular cloning and complete nucleotide sequence of the genome of Japanese encephalitis virus Beijing-1 strain

The genomic RNA of the Japanese encephalitis virus (JEV) Beijing-1 strain was reversely transcribed and the synthesized cDNA was molecularly cloned. Six continuous cDNA clones that cover the entire virus genome were established and sequenced to determine the complete nucleotide sequence of the JEV RNA. The precise genomic size was estimated as 10,965 bases long. With flanking 95 bases at the 5 and 583 bases at the 3 non-coding regions, one long open reading frame (ORF) was revealed encoding a virus polyprotein with 3,429 amino acid residues. Because of sequence homologies observed between JEV and other flaviviruses, the genome organization of JEV appears to be identical with other flaviviruses. Genetic variation detected among flavivirus genomes is consistent with the established serological relatedness between JEV and other members of flaviviruses. The secondary structure of the JEV genome is deduced and discussed concerning its involvement in genome replication.     

Innate immune responses of calves during transient infection with a noncytopathic strain of bovine viral diarrhea virus

In this study, six immunocompetent calves were experimentally infected with a noncytopathic strain of bovine viral diarrhea virus (BVDV), and the effects of the viral infection on parameters of the innate immune response of the host were analyzed. Clinical and virological data were compared with the temporal activation of the alpha/beta interferon-regulated Mx gene in white blood cells (WBC) and skin as well as the upregulation of the acute-phase serum proteins haptoglobin (Hp) and serum amyloid A (SAA). The viral strain used did provoke transient health impairment, namely, fever and leukopenia that were associated with viremia, viral shedding with nasal secretions, and antiviral seroconversion. Complete recovery was observed within 3 weeks. Elevated levels of SAA and Hp were apparent from days 4 to 13 and 8 to 11, respectively. In WBC, the levels of Mx mRNA and Mx protein were elevated from days 2 to 15. In the context of this study with BVDV, the level of Mx protein expression in WBC provided the most telling diagnostic window to monitor the host's ongoing innate immune response.     

Molecular cloning and nucleotide sequence of the genome of hog cholera virus

A cDNA clone derived from genomic RNA of hog cholera virus (HCV) was identified using an oligonucleotide complementary to the RNA encoding a hexapeptide from the putative RNA-dependent RNA polymerase of the closely related bovine viral diarrhea virus (BVDV). This clone served as a probe for screening different size-selected cDNA libraries. After molecular cloning and nucleotide sequencing the HCV genome was shown to consist of 12,284 nucleotides containing one long open reading frame. Sequence comparison revealed a high degree of homology between HCV and BVDV genomic RNAs. With respect to HCV the genome of BVDV contains an insertion coding for 90 amino acids.     

Isolation of bovine viral diarrhea virus 1, a pestivirus from autopsied lamb specimen from Tamil Nadu, India

An epizootic of febrile illness among the Madras red breed of sheep had occurred in 1994 in Verrapuram, Chennai, India. The epizootic was suspected as Rift Valley fever (RVF)-like sickness based on clinical features. However, its etiological agent could neither be isolated nor implicated conclusively. During the post-epizootic period a male lamb died of similar clinical features and the spleen was immediately collected. Inoculation of spleen suspension in infant mouse brain yielded a virus that was serially passaged in infant mice and rhabdomyosarcoma (RD) cells. Electron microscopic observations revealed virus particles resembling flaviviruses. RT-PCR performed on extracted total RNA from infected cells and mouse brains with flavivirus-specific or RVF-specific primers gave negative results. However, an amplicon of 280 bp was obtained with pestivirus-specific primers from the 5'-UTR. Further, a nested PCR yielded a product of 157 bp. Nucleotide sequencing of the 157 bp product showed 100% homology to BVDV-1. Western blot analysis with a flavivirus envelope protein-specific MAb revealed three proteins of 33 K, 45 K and 55 K. Further studies suggested that the 33 K and 55 K proteins were glycosylated. This is the first report of isolation of BVDV-1 from a lamb in India.     

Proteins encoded by bovine viral diarrhea virus: the genomic organization of a pestivirus

The genome of bovine viral diarrhea virus (BVDV) contains a single large open reading frame capable of encoding 449 kDa of protein. Short segments from along the length of the molecularly cloned BVDV genome were engineered so as to be expressed as bacterial fusion polypeptides in Escherichia coli. These BVDV analog fusion proteins were used as immunogens to generate a panel of sequence-specific antisera. These antiserum reagents were in turn employed in immunoprecipitation analyses to identify the authentic BVDV protein to which they were directed. The results allowed for the identification and positioning along the genome of BVDV gene products accounting for approximately 83% of the coding capacity of the virus. A preliminary map of the genetic organization of BVDV is presented and discussed.     

Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome

In present study, we report the first complete genomic sequence of pig bovine viral diarrhea (BVD) virus, that of strain ZM-95, which is 12,220 nucleotides long and contains short 5' and 3' non-coding regions and one open reading frame encoding a large polyprotein with 28 potential N-glycosylation sites (Asn-X-Ser or Asn-X-Thr). Within the non-structural protein encoding region, no foreign nucleotide insertions was found as those usually observed for cytopathogenic BVDV-1, but close to the 3'-terminal of the capsid protein (1119-1124bp) it contains a short insertion of a six nucleotide sequence (CTCACA). Three hypervariable regions were identified in the polyprotein-encoding region, with one of them comprising a sequence motif encoding a unique five amino acid peptide HYKKK in glycoprotein E2 gene. The genomic comparison and phylogenetic analyses showed that ZM-95 should be classified into BVDV-1, but was genetically divergent from other pestiviruses sequenced to date since its highest genetic similarity was only 76.6% (with SD-1), therefore, placed as a novel subgroup of BVDV-1.     

Genetic characterization of a noncytopathic bovine viral diarrhea virus 2b isolated from cattle in China

In January 2013, several clinical signs of cattle with diarrhea, cough, nasal discharge, and fever were reported in Jilin province, China. One virus named SD1301 was isolated and identified. Complete genome of the virus is 12258nt in length and contains a 5′UTR, one open reading frame encoding a polyprotein of 3,897 amino acids and a 3′UTR. Phylogenetic analysis of 5′UTR, N^pro, E1 and E2 gene demonstrated the virus belonged to BVDV 2b, and genetically related to the BVDV strain Hokudai-Lab/09 from Japan in 2010. This bovine viral diarrhea virus displays a unique genetic signature with 27-nucleotide deletion in the 5′UTR, which is similar to the bovine viral diarrhea virus C413 (AF002227). This was the first confirmed isolation of ncp BVDV2b circulating in bovine herd of China.     

汉滩病毒Z10株G1糖蛋白编码区克隆及序列分析

目的 汉滩病毒浙１０（Ｚ１０）株Ｇ１糖蛋白编码区的克隆、核苷酸序列分析，提供我国应用最为广泛的肾综合征出血热（ＨＦＲＳ）疫苗株序列资料。方法 反转录ＰＣＲ法扩增Ｇ１基因片段，克隆入ｐＧＥＭ－Ｔ载体，双脱氧链终止法测定核苷酸序列。结果 测定１４４９个核苷酸，可编码４８３个氨基酸。与Ｉ型７６／１１８、Ｌｅｅ、Ｈｏｊｏ株比较核苷酸同源性分别为８７％、８６％、８６％，与Ⅱ型Ｒ２２株同源性为６７％。比较氨基     

Detection of cytopathic and noncytopathic bovine viral diarrhea virus in cell culture with an immunoperoxidase test

Bovine viral diarrhea virus (BVDV) antigen was detected in cell culture with an indirect immunoperoxidase (IP) procedure using a specific monoclonal antibody, and an avidin-biotin-peroxidase complex. Cytopathic and noncytopathic strains of the virus showed similar patterns of IP staining until 3 days post-infection. At six days post-infection, intensity of staining decreased in cell cultures infected with noncytopathic virus, but not with cytopathic virus. The IP procedure detected BVDV antigen in cells used to isolate virus from tissues of aborted bovine fetuses and peripheral blood lymphocytes of adult cattle. Immunoperoxidase detected BVDV isolates from 10 of 44 cases of abortion of which seven of these were noncytopathic. Noncytopathic BVDV isolates from the peripheral blood lymphocytes of 7 of 65 animals were identified.     

Analysis of the bovine viral diarrhea virus genome for possible cellular insertions.

Mucosal disease is the most severe disease resulting from bovine viral diarrhea virus (BVDV) infection in cattle. Two biotypes of BVDV may be isolated from animals with mucosal disease: cytopathic (cp) and noncytopathic (ncp). These "pairs" of cp/ncp viruses are often closely related and it has been suggested that the cp virus arises from a ncp virus by insertion of cellular RNA in the p125 region of the BVDV genome. We have used four pairs of cp/ncp BVDV isolated from cattle with mucosal disease, to examine the genomic sequence of the region of the genome coding for the nonstructural protein p125 (processed to p54/p80 in cp viruses) by PCR analysis and sequencing. We did not detect any cellular gene insertions in any of the four ncp viruses; however, we found a large duplication of the p80 gene and a ubiquitin gene insertion in three of the four cp isolates. Our results suggest that cellular RNA insertions in the p125 region may contribute significantly to the cytopathogenicity of BVDV. However, this does not appear to be the only mechanism of cytopathogenicity as we did not detect any insertions or duplications in one of the cp viruses. Comparison of the DNA sequence in the p80 region revealed greater homology within the "pairs" than to NADL, which lend further support to the hypothesis that a cp virus is originated from a ncp virus.     

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.     

Molecular cloning and nucleotide sequence of P, M and F genes of Newcastle disease virus avirulent strain D26

Molecular cloning of most if not all of the genome of an avirulent strain D26 of Newcastle disease virus (NDV) was carried out. cDNA clones were aligned by mutual hybridization and restriction map analysis. The nucleotide sequence of 3672 bases which completed the partial sequence of P gene reported in our previous paper (Ishida, N. et al., 1986, Nucleic Acids Res. 14, 6551-6564), and also covered M and F genes, was determined. Each gene contained one long open reading frame which could code for polypeptides of 395, 364, and 553 amino acid residues, respectively. The deduced amino acid sequences of P and M gene products showed little homology to those of other paramyxoviruses. In contrast, comparison of the amino acid sequence of the F gene product revealed highly conserved regions including the amino terminal sequence of the F1 portion following the putative processing site. There was only one basic amino acid residue at the putative processing site, which would explain the low virulence of this strain.     

The genome nucleotide sequence of a contemporary wild strain of measles virus and its comparison with the classical Edmonston strain genome

The only complete genome nucleotide sequences of measles virus (MeV) reported to date have been for the Edmonston (Ed) strain and derivatives, which were isolated decades ago, passaged extensively under laboratory conditions, and appeared to be nonpathogenic. Partial sequencing of many other strains has identified >/=15 genotypes. Most recent isolates, including those typically pathogenic, belong to genotypes distinct from the Edmonston type. Therefore, the sequence of Ed and related strains may not be representative of those of pathological measles circulating at that or any time in human populations. Taking into account these issues as well as the fact that so many studies have been based upon Ed-related strains, we have sequenced the entire genome of a recently isolated pathogenic strain, 9301B. Between this recent isolate and the classical Ed strain, there were 465 nucleotide differences (2.93%) and 114 amino acid differences (2.19%). Computation of nonsynonymous and synonymous substitutions in open reading frames as well as direct comparisons of noncoding regions of each gene and extracistronic regulatory regions clearly revealed the regions where changes have been permissible and nonpermissible. Notably, considerable nonsynonymous substitutions appeared to be permissible for the P frame to maintain a high degree of sequence conservation for the overlapping C frame. However, the cause and the effect were largely unclear for any substitution, indicating that there is a considerable gap between the two strains that cannot be filled. The sequence reported here would be useful as a reference of contemporary wild-type MeV.     

Molecular cloning and complete nucleotide sequence of galinsoga mosaic virus genomic RNA

Summary.  The complete genomic sequence of galinsoga mosaic virus (GaMV) was determined. The genome consists of 3 803 nucleotides and has five open reading frames (ORFs). The 5′ ORF (ORF 1) encodes a protein with predicted molecular mass of 23 kDa and readthrough of its amber stop codon probably yields a 82 kDa protein (ORF 2). ORFs 3 and 4 encode two polypeptides with molecular masses of 8 and 7 kDa, respectively. ORF 5 encodes the 36 kDa capsid protein. Amino acid sequence comparisons revealed that the nonstructural proteins encoded by ORFs 1, 3, and 4 were more similar to the corresponding gene products of tobacco necrosis virus, strain A, than to those of carmoviruses. Conversely, the coat protein was more similar to that of tombusviruses. The readthrough region of the viral replicase (ORF 2) had high sequence homology with that of carmo-, tombus-, and necroviruses. Computer analysis of the protein encoded by ORF 1 as well as of the corresponding product of turnip crinkle (TCV) and melon necrotic spot (MNSV) carmoviruses revealed the presence of a sequence with local hydrophobicity and hydrophobic moment characteristic of mitochondrial targeting sequence which may explain the origin of the carmovirus-induced multivesicular bodies from mitochondria. Accepted August 25, 1997 Received June 18, 1997     

Genomic characterization of a bovine viral diarrhea virus 1 isolate from swine

The SD0803 strain of the bovine viral diarrhea virus (BVDV) was isolated from a piglet in China in 2008 and has been classified as a novel subgenotype of BVDV-1. To describe the molecular features of this novel subgenotype, we sequenced and characterized the complete genome of the SD0803 virus. The genome is 12,271 bp in length and contains 5′ and 3′ untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a 3,898-amino-acid polypeptide. The full-length genome of the SD0803 strain shares 78.8 % to 83.3 % identity with those of other BVDV-1 strains, 70.0 % to 70.7 % identity with those of BVDV-2 strains, and less than 67.6 % identity with those of other pestiviruses. The highest level of shared identity was 83.3 % between the complete SD0803 genome and that of the ZM-95 strain of BVDV-1. Phylogenetic analysis of the 5′ UTR and the coding sequence for the N-terminal protease fragment of the SD0803 polyprotein indicated that the SD0803 virus is a member of the novel subgenotype BVDV-1q, isolates of which have been identified recently in dairy cattle and camels in China.     

Molecular cloning and nucleotide sequence of hog cholera virus strain Brescia and mapping of the genomic region encoding envelope protein E1

Genomic RNA of hog cholera virus (HCV) strain Brescia was cloned and sequenced. The nucleotide sequence was deduced from overlapping cDNA clones and comprises 12,283 nucleotides. We cloned the complete 3' end of the HCV genome, but could not unequivocally prove that the cDNA sequence also completely covers HCV RNA at the 5' end. The HCV genome contained one large open reading frame, which spans the viral plus strand RNA and encodes an amino acid sequence of 3898 residues with a calculated molecular weight of 438,300. To identify structural HCV glycoproteins, we prepared rabbit antisera against three synthetic peptides deduced from the sequence. Because one of these antisera reacted with a 51- to 54-kDa glycoprotein (envelope protein E1 of HCV) on Western blot, the genomic position of the sequence encoding gp51-54 could be clearly established. The amino acid sequence of Brescia was compared with that of HCV strain Alfort and that of BVDV strains NADL and Osloss. The degree of homology between the two HCV strains was 93%, and between Brescia and the BVDV strains about 70%. NADL contained an inserted sequence of 90 amino acids that was absent from the sequences of Brescia, Alfort, and Osloss, whereas Osloss contained an inserted sequence of 76 amino acids that was absent from the sequences of Brescia, Alfort, and NADL. Sequences in p80, the most homologous protein among pestiviruses, showed similarity to six sequence motifs found conserved in helicase-like proteins represented by eIF-4A. Furthermore, a trypsin-like serine protease domain detected in p80 of BVDV was also found conserved in HCV, suggesting that pestivirus p80 may be bifunctional.     

Soluble antigen of bovine viral diarrhea virus

Summary Complement-fixing (CF) soluble antigen (SA) was detectable intra-cellularly prior to the appearance of infectious NADL-MD bovine viral diarrhea (BVD) virus during synthesis in roller flask cultures of bovine embryonic kidney cells. The release of infective virus into the extracellular fluid was concomitant with the release of SA.The SA was separated from the infective virus by sedimentation in a sucrose density gradient and by DEAE-cellulose chromatography.The SA was heat labile at 56° C, but stable in buffers at pH 5, 7, and 9 at 37° C. The SA was irreversibly precipitated in buffers at pH of 3 or below.Trypsin and -chymotrypsin completely inactivated the SA, whereas ribonuclease and deoxyribonuclease had no detectable effect on the CF activity.There was no apparent CF or neutralizing relationship between the SA and infectious NADL-MD BVD virus and arbovirus group B and lymphocytic choriomeningitis virus antisera.