Hybridization analysis of genomic variability among isolates of bovine viral diarrhoea virus using cDNA probes

Genetic typing of bovine viral diarrhea virus isolates from Argentina

Genetic typing of 29 Bovine Viral Diarrhea Virus (BVDV) isolates from Argentina was carried out by sequencing 245 nucleotides of the RT-PCR products of the 5'-UTR region. Sequence analysis shows that these Argentinean BVDV include types 1 and 2. The majority (26/29) of the isolates are type 1, which comprises subtypes 1a and 1b, together with an additional subgroup within subtype 1a. This subgroup is close to the South African subgroup Ic of 1a viruses, and to the deer pestivirus strain "Deer". The three type 2 BVDV were isolated from fetal tissues or serum during the 7-8 years before a clinical outbreak in Argentina had been reported. Only inactivated vaccines are used in bovines of the country, thus the analysed viruses are authentic field strains. The long term circulation of type 2 BVDV (situation similar to that of North America before the epidemic of 1993), and the existence of viral populations which differ from the reference strains commonly used in vaccine elaboration should be considered by manufacturers of diagnostic reagents and vaccines.

Genetic heterogeneity of bovine viral diarrhoea viruses isolated in Southern Africa

Seventy three field isolates of bovine viral diarrhoea virus (BVDV), obtained from cattle in Mozambique and South Africa, were characterised by comparative nucleotide sequence analysis of part of the 5' non-coding region (5'NCR) of the viral genome. The target region was amplified by reverse transcription-polymerase chain reaction (RT-PCR). The amplicons were cloned in pUC 19 plasmid and both strands were sequenced by T7 polymerase dideoxynucleotide chain-termination sequencing or directly by cycle sequencing. The 245 base pair (bp) nucleotide sequences, derived from the 5'NCR, were aligned and compared to the corresponding positions of published sequences of BVDV type I and II strains and of pestiviruses of ovine and porcine origin. The phylogenetic trees, generated from those comparisons, allowed the Southern African isolates to be assigned to two main groups within the BVDV I genotype. Group A could be subdivided into three clusters, two of which grouped with BVDV strains of European and American origin. The third cluster did not group with any known BVDV I strains and it was confirmed in a comparison from the NS3 coding region. Group B contained more divergent isolates which differed by 18-23%, from BVDV I reference strains NADL, Osloss and SD-1 and comprised another distinct subset within the BVDV I genotype. This grouping was consistent in a comparison involving the NS2-NS3 region. It was concluded that BVD viruses occurring in Southern Africa are genetically diverse, comprising different variants within the BVDV I genotype. They include viruses similar to BVDVs found in Europe and America and others apparently rare or absent in those continents, termed here as BVDV Ic and Id. The co-existence of BVDV strains of European and American origin in certain areas both in Mozambique and South Africa, indicates a probable introduction of those viruses through imports of cattle or through potentially infectious bovine products. In addition, the detection of isolates apparently rare or absent from Europe and America may indicate the presence of African variants of BVDV I (Pestivirus 1).

Comparative study on four enzyme-linked immunosorbent assays and a cocultivation assay for the detection of antigens associated with the bovine viral diarrhoea virus in persistently infected cattle

Four commercially available ELISAs for detection of antigens associated with the bovine viral diarrhoea virus in persistently infected cattle have been compared. The tests are equally specific (100%) and the sensitivity of three ELISAs is comparable with that of a conventional cocultivation assay. Performing ELISA on samples from young animals that received colostrum may yield false negative results because of interference of maternal antibodies in the tests. It is concluded that ELISA can be a valuable tool in eradications programs when large numbers of cattle are to be monitored.

The pathologies of bovine viral diarrhea virus infection. A window on the pathogenesis

Pathologic lesions caused by bovine viral diarrhea virus (BVDV) infections comprise a wide spectrum of type, degree, and, by implication, pathogenesis, including congenital defects, necroticerosive lesions in mucosal epithelia and skin, and reactive as well as degenerative changes in lymphoid tissues. At least some of the pathology may not be solely due to BVDV replication per se, but rather caused by a host response to the virus, particularly the production of pro-inflammatory cytokines.

Rapid detection of bovine viral diarrhea virus by using RNA extracted directly from assorted specimens and a one-tube reverse transcription PCR assay

We describe a simple method for the rapid detection of bovine viral diarrhea virus (BVDV) that uses a one-tube reverse transcription PCR (RT-PCR) and total RNA extracted directly from a variety of bovine specimens, including whole blood and tissues. Reagents for both RT and PCR were combined in a one-tube, single-buffer system, and amplification was performed with a single uninterrupted thermal cycling program. Using the novel cationic surfactant tetradecyltrimethylammonium oxalate (Catrimox-14), we consistently extracted RT-PCR-quality RNA from specimens containing blood. Amplification with primers derived from conserved sequences within the BVDV 5'-untranslated region yielded a 244-bp product. Assay specificity was confirmed by ethidium bromide-stained gel electrophoresis and by chemiluminescence-assayed Southern blot hybridizations involving BVDV 5'-untranslated region-specific digoxigenin-labelled cDNA probes. The assay detection level was 0.1 50% tissue culture infectious dose of BVDV when ethidium bromide-stained gel electrophoresis was used and 0.01 50% tissue culture infectious dose of BVDV when Southern blot hybridization was used. Our method is an alternative to the conventional cell culture assays used in a diagnostic laboratory and is an improvement over existing RT-PCR assays for BVDV.

Ruminant pestiviruses

The ruminant pestiviruses, bovine virus diarrhoea virus (BVDV) and border disease virus (BDV) are highly successful and important pathogens which infect ruminant species worldwide. Although the serological relationships among ruminant pestiviruses require further clarification, there is growing evidence for two antigenic groups, one of which predominates in cattle and one in sheep. The success of pestiviruses stems from the ability of the non-cytopathic (NCP) biotype of the virus to cross the placenta and establish a persistent infection (PI) in the developing foetus. This biotype should be regarded as the 'normal' biotype with the cytopathic (CP) biotype being an abnormal virus that is usually isolated only from PI animals dying from mucosal disease. Recent molecular evidence points to CP viruses arising from their NCP counterparts by recombination events that include the insertion of host RNA and/or the duplication of viral RNA sequences. However, the biological mechanism through which CP viruses kill cells remains unknown. Virtually all CP and NCP viruses cause only mild, transient clinical symptoms in healthy adult animals and stimulate a protective immune response. Despite the urgent requirement for a safe, effective vaccine, there is still no commercial vaccine that has been shown to immunize dams so that foetal infection is prevented. In the absence of an effective vaccine, reliable diagnostic techniques are essential to implement effective control measures. There is now a range of monoclonal antibody-based enzyme-linked immunosorbent assays for identifying PI or convalescent animals. These tests are specific, rapid, sensitive and reliable but may themselves become redundant as they are superceded by ever-increasing molecular biology-based techniques.

Evaluation of a 'one tube' reverse transcription-polymerase chain reaction for the detection of ruminant pestiviruses

A 'one tube' reverse transcription-polymerase chain reaction ('one tube' RT-PCR) using rTth DNA polymerase was compared with an existing RT-PCR using Taq DNA polymerase (Taq RT-PCR) to detect ruminant pestiviruses in infected cell cultures. The technically simpler and more convenient 'one tube' method was relatively insensitive detecting only 11 of the 34 samples tested, all of which were positive by Taq RT-PCR.

Pestiviruses isolated from pigs, cattle and sheep can be allocated into at least three genogroups using polymerase chain reaction and restriction endonuclease analysis

A polymerase chain reaction-based assay capable of detecting a broad range of pestiviruses from pigs, cattle, or sheep was developed. Of six sets of primers selected from different parts of the pestivirus genome, the best results were provided by a pair from the highly conserved 5' non-coding region which gave amplification with all 129 isolates tested. This panel consisted of 33 isolates from pigs, 79 from cattle, and 17 from sheep. Differentiation between the viruses was achieved by cutting the PCR-amplified products with the restriction endonucleases AvaI and Bg1I. Using this procedure it was possible to distinguish at least 3 genogroups; group 1 (HCV) contained 32 of the pig isolates, group II (BVDV) contained all the cattle isolates tested plus 6 sheep isolates and group III (BDV) contained 11 sheep isolates and 1 pig isolate.

Survey of cell lines in the American Type Culture Collection for bovine viral diarrhea virus

Cell lines originating from cattle, sheep, goat, deer, bison, swine, rabbit, hamster, cat, dog, monkey, human, and mosquito were obtained from the American Type Culture Collection and tested for contamination with bovine viral diarrhea virus (BVDV). Immunocytochemical procedures and polymerase chain reaction (PCR) amplification were used to detect viral antigen or viral RNA in 13 of 41 cell lines. The results of these procedures correlated exactly. Cell lines derived from cattle, sheep, goat, deer, bison, rabbit, and domestic cat were found contaminated with BVDV. Attempts were made to experimentally infect 14 swine, rabbit, hamster, cat, dog, monkey, and human cell lines that had been found free of virus. All swine cell lines, and most rabbit and cat cell lines, became infected with BVDV. Hamster, human, dog, and certain rabbit and cat cells were refractory to BVDV infection. Experimental infection of monkey cells produced variable results.

Analysis of capsid protein gene variation among divergent isolates of feline calicivirus

Genomic variability within the capsid protein gene of feline calicivirus (FCV) was evaluated among different isolates using hybridization analysis and enzymatic viral nucleic acid amplification. Total infected cell RNA was first hybridized with cDNA clones generated to the capsid gene of the FCV isolates CFI/68, 255, LLK, NADC and KCD. Field isolates of FCV were categorized by hybridization with capsid gene cDNA from the reference strains. Isolates that did not hybridize were positive by Western blot using a cross-reactive cat polyclonal FCV CFI/68 capsid protein antiserum. Using previously published sequence information, oligonucleotide primers were generated based on conserved sequences surrounding the hypervariable capsid protein gene regions. Analysis of the FCV capsid protein gene hypervariable regions was completed by sequencing products of FCV nucleic acid amplified by reverse transcription and polymerase chain reaction. From these data, amino acid substitutions in the hypervariable regions of the capsid protein were identified for those isolates that did not hybridize with the original cDNA clones. An association between phylogenetic relationships and serum neutralization was established among FCV isolates examined.

Natural recombination in bovine viral diarrhea viruses

BVDV isolates exist as two biotypes differentiated at the molecular level by production of a p80 polypeptide. Insertions consisting of host cell sequences and/or duplicated and rearranged viral sequences have been observed in the portion of the genome coding for the p80 polypeptide in some, but not all, cytopathic BVDV. The significance of these insertions to biotypic expression has yet to be demonstrated. It has been hypothesized that recombination results in the production of the p80 polypeptide by introduction of a cleavage site into a precursor polypeptide or the introduction of a second copy of the p80 gene. Because inserts have not been identified in all cytopathic BVDV examined, it appears that recombination may not be the only mechanism involved in biotypic determination.

Comparative hybridization and nucleotide sequence information from two noncytopathic isolates of bovine viral diarrhea virus

Comparative hybridizations of 8 cytopathic (CP) and 11 noncytopathic (NCP) isolates of bovine viral diarrhea virus (BVDV) were done using 4 different cDNA hybridization probes. The hybridization probes were prepared from cDNA synthesized from 1 CP BVDV (NADL) and 2 NCP BVDV isolates (SD-1 and NY-1) within the p80 region and from cDNA spanning the 5' untranslated region of NCP SD-1. Hybridization with the 5'/SD-1 probe detected 19 out of 19 isolates, whereas the p80/NADL, p80/NY-1 and p80/SD-1 hybridization probes detected only 12, 16 and 13 isolates, respectively. To determine the basis for the different patterns of hybridization, the nucleotide sequence was determined for the p80/NY-1. The nucleotide sequence was compared with the published CP NADL and CP Osloss and NCP SD-1 and NCP1 nucleotide sequences and in 45% of the base differences between NY-1 and NADL, NY-1 and Osloss were divergent from NADL, SD-1 and NCP1. Based on comparative nucleotide sequence data and the different reactivities of the p80/NADL, p80/NY-1 and p80/SD-1 hybridization probes the relationships of the various test isolates were characterized.

Comparison of nucleic acid hybridization and nucleic acid amplification using conserved sequences from the 5' noncoding region for detection of bovine viral diarrhea virus

Primers and probes derived from conserved sequences located in the 5' noncoding region of pestiviruses were evaluated for detection of bovine viral diarrhea virus. With these reagents, hybridization and polymerase chain reaction tests detected 62 of 90 and 90 of 90 bovine viral diarrhea virus isolates, respectively. A quick lysis method for preparing RNA for use in polymerase chain reaction amplification also was evaluated.

Presumptive diagnostic differentiation of hog cholera virus from bovine viral diarrhea and border disease viruses by using a cDNA nested-amplification approach

Hog cholera virus (HCV), bovine viral diarrhea virus (BVDV), and border disease virus (BDV) are closely related pestiviruses. BVDV and BDV are found worldwide but seldom cause disease in swine. In contrast, HCV has been successfully eradicated from swine in several nations but poses a potentially devastating threat to them because of its great virulence. Rapid differential diagnosis of HCV from BVDV and BDV infections in swine is vital for detection of the possible reintroduction of HCV into national herds from which it has been eradicated. Nested polymerase chain reactions (PCRs) for each of two pestiviral genomic segments are described. Amplification of the relatively conserved 5' genomic terminus identified 59 of 61 HCV, BVDV, and BDV isolates generically as pestiviruses. Nested amplification of the second region was designed to differentiate HCV from BVDV and BDV by exploiting relatively conserved differences in the nucleotide sequences that encode the major envelope glycoprotein. This second PCR correctly identified 36 of 36 diverse HCV isolates while failing to recognize any of 25 BVDV and BDV isolates. Multiple restriction fragment length analyses confirmed the identities of both external and nested PCR products. The two sets of PCRs may help confirm the generic identity of most pestiviruses and may permit presumptive differential diagnosis of HCV from BVDV and BDV.

Nucleotide sequencing of 5' and 3' termini of bovine viral diarrhea virus by RNA ligation and PCR

Genomic RNA was extracted from cytopathic (CP) bovine viral diarrhea virus (BVDV) strain NADL, CP strain 72, and noncytopathic (NCP) strain SD-1 purified by ultracentrifugation. Assuming the presence of a cap structure, de-blocking of the 5' capped end of the genomic RNA was done by treatment with tobacco acid pyrophosphatase (TAP). Following decapping, the RNA molecules were ligated using T4 RNA ligase and the ligated tandem RNA templates were then amplified by primer-directed amplification (PCR). cDNA synthesis was done using reverse transcriptase with random primers and cDNA amplification was done using a negative sense primer 231-248 and a positive sense primer 12434-12451. The nucleotide sequence of the amplified product was determined by double-stranded sequencing using the Sanger di-deoxy chain termination method and an additional 'CCCCC' nucleotide sequence was identified at the ligation site. Following dATP tailing of cDNA and amplification across the 5' terminus and nucleotide sequencing, no additional nucleotides were identified on the 5' terminus. The 5' terminus as published by Collett et al., 1988b was confirmed as previously reported. Therefore, the 3' terminus includes an additional 'CCCCC' nucleotide sequence to that previously reported. Identical results were obtained when the BVDV genomic RNA was not decapped prior to RNA ligation and amplification.