Genetic heterogeneity of bovine viral diarrhoea viruses isolated in Southern Africa

First-time detection of bovine viral diarrhoea virus, BVDV-1, in cattle in Botswana

Infectious diseases are serious constraints for improving livestock productivity. Bovine viral diarrhoea virus (BVDV) is a virus causing grave economic losses throughout the cattle producing world. Infection is often not apparent, but the virus can also cause respiratory signs, diarrhoea, reproductive problems and immunosuppression. Risk factors for disease transmission include, but are not limited to, herd size, animal trade and grazing on communal pastures. Several prevalence studies have been conducted in southern Africa, but in Botswana the occurrence is largely unknown. In this study, blood samples were obtained from 100 goats from three villages around the capital city, Gaborone. Also, 364 blood samples from cattle around Gaborone, collected as part of another study, were analysed. The detected antibody prevalence was 0% in goats and 53.6% in cattle when using a competitive enzyme-linked immunoassay. Three animals from two different herds were positive for viral nucleic acids on polymerase chain reaction. The two herds with viraemic animals had significantly higher antibody prevalence compared to the other herds. Also, two of the detected viruses were sequenced and found to be most similar to BVDV-1a. To the authors' knowledge, this is the first time that sequencing has been performed on BVDV isolated in Botswana.

Who's who in the Bovine viral diarrhea virus type 1 species: Genotypes L and R

The bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, with relevant impact on animal production. The species presents high genomic heterogeneity, with implications on control and prophylactic programs. Genomic traits of different genetic groups are often related to geographic origin. Atypical sequences have been reported from Pestivirus isolates originated from cattle in Turkey. Based on phylogenetic analysis of 5' untranslated region and Npro and secondary structure analysis of the 5'-UTR RNA, Turkish isolates have been segregated in two distinct genotypes. Out of the twenty-three identified BVDV-1 genotypes, the Turkish clusters, named L and R or 1.16 and 1.14, according to palindromic nucleotide substitution genotyping method, represent genomic clusters so far, not described elsewhere, suggesting geographic segregation. In order to avoid confusion in the current taxonomy of the species, nomenclature of described homonymous genotypes, referred to different genomic clusters, should be corrected.

Bovine viral diarrhea virus type 1 current taxonomy according to palindromic nucleotide substitutions method

Pestivirus bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, presenting a wide range of clinical manifestations, with relevant impact on zootechnic production. Understanding genomic characteristic and virus taxonomy is fundamental in order to sustain control and prophylactic programs. Given the recent various studies reporting a relatively high number of new strains, in particular from Asian countries, in the present study, four hundred-eighty-two genomic sequences have been evaluated applying the palindromic nucleotide substitutions method for genotyping. Based on the secondary structure alignment and computing genetic distance among strains in the 5' untranslated region of Pestivirus RNA, the current taxonomy of the species was reviewed. Twenty-two genotypes have been identified, applying a nomenclature based on divergence in the genus.

Variability and Global Distribution of Subgenotypes of Bovine Viral Diarrhea Virus

Bovine viral diarrhea virus (BVDV) is a globally-distributed agent responsible for numerous clinical syndromes that lead to major economic losses. Two species, BVDV-1 and BVDV-2, discriminated on the basis of genetic and antigenic differences, are classified in the genus Pestivirus within the Flaviviridae family and distributed on all of the continents. BVDV-1 can be segregated into at least twenty-one subgenotypes (1a–1u), while four subgenotypes have been described for BVDV-2 (2a–2d). With respect to published sequences, the number of virus isolates described for BVDV-1 (88.2%) is considerably higher than for BVDV-2 (11.8%). The most frequently-reported BVDV-1 subgenotype are 1b, followed by 1a and 1c. The highest number of various BVDV subgenotypes has been documented in European countries, indicating greater genetic diversity of the virus on this continent. Current segregation of BVDV field isolates and the designation of subgenotypes are not harmonized. While the species BVDV-1 and BVDV-2 can be clearly differentiated independently from the portion of the genome being compared, analysis of different genomic regions can result in inconsistent assignment of some BVDV isolates to defined subgenotypes. To avoid non-conformities the authors recommend the development of a harmonized system for subdivision of BVDV isolates into defined subgenotypes.

Genetic and Clinical Analyses of Bovine Viral Diarrhea Virus Isolates from Dairy Operations in the United States of America

To assess the prevalence of bovine viral diarrhea virus (BVDV) on the basis of the genotype and clinical signs, isolates from 16 dairy herds (bulk milk samples) and 37 BVDV-infected cattle were examined. Isolates for this study were selected from submissions that contained an adequate clinical history. A part of the E2 gene of BVDV from these isolates was amplified by reverse transcription-polymerase chain reaction. From the nucleotide sequence of the amplified products, phylogenetic analyses were performed and genotypes or subgenotypes were identified. Forty percent of the selected field isolates were BVDV-2, and 60% were BVDV-1. Eighty-one percent of BVDV-1 isolates were determined to be the BVDV-1b subgenotype. BVDV-1b and BVDV-2 formed more closely related clusters in each group than did the BVDV-1a isolates. There was no obvious association of any genotype or subgenotype with geographical localization or clinical manifestations. A higher prevalence of BVDV-2 infection was found in the United States than in other countries. BVDV-1a has been thought of as a prototype of BVDV; however, there were fewer isolations of BVDV-1a than of other subgenotypes of BVDV Phylogenetic analyses of BVDV isolates using the E2 region of the genome generated results similar to those of studies done in the United States using the 5' untranslated region.

Genotypic characterization of Chilean llama (Lama glama) and alpaca (Vicugna pacos) pestivirus isolates

Llamas and alpacas are domesticated South American camelids (SACs) important to ancestral population in the Altiplano region, and to different communities worldwide where they have been introduced. These ungulates have shown to be susceptible to several livestock viral pathogens such as members of the Pestivirus genus, in particular Bovine Viral Diarrhea (BVDV), but there is little data available on Pestivirus infections in SACs. In this study we aimed to detect and identify Pestivirus genotypes and subgroups infecting SACs in both wild and confined environments. Samples were collected from 136 llamas and 30 alpacas from different areas in the Chilean Altiplano (wild animals), and from 22 llamas and 26 alpacas diagnosed as Pestivirus positive from the Metropolitana region in Chile (confined animals). Seroneutralization tests showed titers lower than 2 in all 166 samples from Chilean Altiplano. These samples were also negative to BVDV isolation, indicating that these animals have not been exposed to Pestivirus. After reactivation of positive samples from the Metropolitana region, the 5' non-codifying region (5'NCR) and E2 glycoprotein were amplified by RT-PCR from the Pestivirus genome. Viral sequences were pairwise compared and phylogenetic trees were constructed. The 5'NCR analysis showed that all 12 sequenced isolates belonged to BVDV-1. Of particular interest, isolates from eight llama and two alpaca were BVDV-1j and two alpacas were BVDV-1b. In agreement with these results, E2 phylogenetic analysis rendered a similar grouping indicating that all 16 isolates belong to BVDV-1. However, the lower availability of E2 sequences determines the creation of a smaller number of sub-groups than the 5'NCR sequences. Based on the E2 sequences, the 5'NCR BVDV 1j group consisting of all the llamas and 3 alpacas are completely included in the E2 BVDV 1e group. Due to the universal availability of the 5'NCR segment, we propose the classification of these Chilean llamas and alpacas Pestivirus isolates as BVDV 1j and BVDV 1b respectively. Thus, this is the first time BVDV-1j is obtained in SACs. In addition, these results indicate Pestivirus infection in llamas and alpacas is associated with bovine population as genotypes and sub-groups are the same as those affecting Chilean livestock.

Antigenic variability in bovine viral diarrhea virus (BVDV) isolates from alpaca (Vicugna pacos), llama (Lama glama) and bovines in Chile

Llamas and alpacas are domesticated South American camelids (SACs) important to ancestral population in the Altiplano region, and to different communities where they have been introduced worldwide. These ungulates have shown to be susceptible to several livestock viral pathogens such as members of the Pestivirus genus and mainly to bovine viral diarrhea virus (BVDV). Seventeen Chilean BVDV isolates were analyzed by serum cross neutralization with samples obtained from five llama, six alpacas, three bovines, plus three reference strains belonging to different subgroups and genotypes. The objective was to describe antigenic differences and similarities among them. Antigenic comparison showed significant differences between different subgroups. Consequently, antigenic similarities were observed among isolates belonging to the same subgroup and also between isolates from different animal species belonging the same subgroup. Among the analyzed samples, one pair of 1b subgroup isolates showed significant antigenic differences. On the other hand, one pair of isolates from different subgroups (1b and 1j) shared antigenic similarities indicating antigenic relatedness. This study shows for the first time the presence of antigenic differences within BVDV 1b subgroup and antigenic similarities within 1j subgroup isolates, demonstrating that genetic differences within BVDV subgroups do not necessary corresponds to differences on antigenicity.

A phylogenetic analysis of Bovine Viral Diarrhoea Virus (BVDV) isolates from six different regions of the UK and links to animal movement data

Bovine Viral Diarrhoea Virus (BVDV) is a pestivirus which infects cattle populations worldwide and is recognised as a significant source of economic loss through its impact on health and productivity. Studies investigating the molecular epidemiology of BVDV can give invaluable information about the diversity of viral strains present in a population and this, in turn, can inform control programs, drive vaccine development and determine likely infection sources. The current study investigated 104 viral isolates from forty farms across the UK. Through phylogenetic and nucleotide sequence analysis of the 5′UTR and N^pro regions of the isolates investigated, it was determined that BVDV 1a was the predominant sub-genotype. However, BVDV 1b, 1e and 1i were also identified and, for the first time in the UK, BVDV 1d. Through analysis of animal movement data alongside the phylogenetic analysis of these BVD isolates, it was possible to link animal movements to the viral isolates present on several premises and, for the first time, begin to elucidate the routes of viral transmission. With further work, this type of analysis would enable accurate determination and quantification of the true biosecurity risk factors associated with BVDV transmission.

Genetic characterization of bovine viral diarrhoea (BVD) viruses: confirmation of the presence of BVD genotype 2 in Africa

Bovine viral diarrhoea virus (BVDV) has emerged as one of the economically important pathogens in cattle populations, with a worldwide distribution and causing a complex of disease syndromes. Two genotypes, BVDV 1 and 2, exist and are discriminated on the basis of the sequence of the 5' non-coding region (5' NCR) using real-time PCR. Real-time PCR is more sensitive, specific, and less time-consuming than conventional PCR, and it has less risk of cross-contamination of samples. Limited information exists on BVDV genetic subtypes in South Africa. The aim of this study was to determine the genotypes of BVDV currently circulating in South African feedlots. A total of 279 specimens (219 tissue samples, 59 trans-tracheal aspirates and 1 blood sample) were collected from dead and living cattle with lesions or clinical signs compatible with BVDV infection. Pooled homogenates from the same animals were prepared, and total RNA was extracted. A screening test was performed on the pooled samples, and positive pools were investigated individually. A Cador BVDV Type 1/2 RT-PCR Kit (QIAGEN, Hilden, Germany) was used for the real-time PCR assay on a LightCycler(®) V2.0 real-time PCR machine (Roche Diagnostics, Mannheim, Germany). The results were read at 530 and 640 nm for BVDV 1 and 2, respectively. Bovine viral diarrhoea virus was detected in a total of 103 samples that included 91 tissue samples, 1 blood sample and 11 trans-tracheal aspirates. Eighty-five (82.5 %) of the strains were genotype 1 and 18 (17.5 %) were genotype 2. Comparing the sequencing data, genotypes 1 and 2 from the field strains did not cluster with vaccine strains currently used in feedlots in South Africa. The present study revealed the presence of BVDV genotype 2 in cattle in South Africa based on the high sequence similarity between genotype 2 field strains and strain 890 from North America. The presence of genotype 2 viruses that phylogenetically belong to different clusters and coexist in feedlots is consistent with the possibility of multiple virus introductions. These results represent the first documented evidence for the presence of BVDV genotype 2 in African cattle.

Hobi-like pestivirus: both biotypes isolated from a diseased animal

A Hobi-like pestivirus pair consisting of cytopathogenic (cp) and non-cytopathogenic (noncp) strains, Italy 83/10cp and Italy 83/10ncp, was isolated from the lung of a heifer that died of respiratory disease. The noncp and cp viruses were isolated on Madin-Darby bovine kidney cells and separated by plaque purification and end point dilution. Analysis of the nearly full-length genomes revealed that the two viruses were very closely related to each other and to the noncp Hobi-like strain Italy 1/10-1, which had been isolated a few weeks earlier from the same herd. One major difference between noncp and cp viruses concerned the presence of a cellular Jiv sequence in the 3' domain of the NS2-encoding region of the cp strain. This is the first study, to our knowledge, reporting the isolation and molecular characterization of a Hobi-like virus pair.

Antigenic relationships between Bovine viral diarrhea virus 1 and 2 and HoBi virus

The emergence of a newly recognized group of pestiviruses in cattle, the HoBi-like viruses, requires an evaluation of the available diagnostic tools and vaccines. The present study compared antigenic characteristics of Bovine viral diarrhea virus 1 and 2 (BVDV-1, -2) strains and HoBi virus. This comparison was based on detection of HoBi virus and antibodies against it by commercial enzyme-linked immunosorbent assays (ELISAs) and the level of cross-neutralizing antibodies present in sera from animals vaccinated with BVDV. Reactivity with a panel of monoclonal antibodies (mAbs) revealed greater cross-reactivity between BVDV species (BVDV-1, -2) and HoBi epitopes within Erns and NS2/3 proteins than between epitopes located in the E2 glycoprotein. The results suggest that a diagnostic test designed to detect both BVDV species and HoBi could be based on Erns or NS2/3 epitopes, while variation among E2 epitopes could be exploited in tests for differentiation of pestivirus species. The threshold of detection of HoBi virus by an antigen-capture ELISA kit based on detection of Erns was statistically similar to that for BVDV. In contrast, 2 commercial ELISA kits designed to detect antibodies against BVDV missed 22.2% and 77.7%, respectively, of serum samples harboring HoBi virus-neutralizing antibodies. In addition, sera of calves vaccinated with BVDV-1 and -2 presented low neutralizing activity against HoBi virus. The results demonstrate that in spite of antigenic similarities, HoBi virus is antigenically distinct from both BVDV species. Detection and control of HoBi virus infections in cattle would thus require the development of new diagnostic reagents and reformulation of current vaccines.

A nested PCR approach for unambiguous typing of pestiviruses infecting cattle

An atypical pestivirus (‘Hobi’-like pestivirus, putative bovine viral diarrhoea 3, BVDV-3) was identified firstly in contaminated foetal calf serum batches and isolated subsequently from an outbreak of respiratory disease in a cattle herd in Italy. The isolation of the novel pestivirus from animals affected clinically posed concerns about the validity of BVDV eradication programs, considering that ‘Hobi’-like pestivirus (BVDV-3) is undetected or mistyped by the molecular diagnostic tools currently employed. In this paper, the development of a nested PCR (nPCR) assay for unambiguous typing of all bovine pestiviruses is reported. The assay consisted of a first-round amplification using an oligonucleotide pair which binds to conserved sequences located in the 5′ untranslated region and capsid gene, followed by a heminested PCR using virus-specific forward primers. The assay performances were evaluated analytically, showing good sensitivity and specificity. By analysis of 100 BVDV-positive samples typed using a nPCR assay discriminating ruminant pestiviruses, five samples recognised previously as BVDV-2 were not typed when submitted to the new assay (n = 2) or reacted as ‘Hobi’-like pestivirus BVDV-3 (n = 3). Sequence analysis of the first-round amplification products showed that the untyped strains were border disease viruses, whereas the other three strains were true ‘Hobi’-like viruses. The development of a molecular assay able to identify simultaneously all bovine pestiviruses known currently will help warrant biosafety of live vaccines and other biological products and assess the molecular epidemiology of ‘Hobi’-like pestivirus, thus leading to the improvement of the eradication programs through unambiguous typing of pestiviruses infecting cattle.

Characterization and Phylogenetic Analysis of Bovine Viral Diarrhea Virus in Brain Tissues from Nonambulatory (Downer) Cattle in Korea

Between August 2008 and May 2009, 386 brain and serum samples from adult cattle (2–7 years old) showing a variety of clinical signs of downer cow syndrome were received by the National Veterinary Research and Quarantine Service. All brain samples were tested for the presence of Bovine viral diarrhea virus (BVDV) by reverse transcription polymerase chain reaction (RT-PCR), immunohistochemistry (IHC), and antigen capture ELISA (Ag-ELISA). The BVDV nucleic acid was detected in 54 of 386 (15.5%) brain samples tested by RT-PCR. Positive results were detected in 14 (3.67%) and 13 (3.4%) of samples tested by IHC and Ag-ELISA, respectively. Both BVDV nucleic acid and antigen were detected in 11 cattle (2.9%) by all 3 diagnostic tests; however, antibodies against BVDV were not detected in these 11 cattle. A molecular classification of the identified viral strains ( n = 40) was also carried out. Neighbor-joining phylogenetic analysis revealed that most of the identified viruses belonged to BVDV genotype 1a ( n = 10), 1b ( n = 16), and 2a ( n = 8). The remaining strains were subtypes 1c ( n = 1), 1n ( n = 4), and 1m ( n = 1). Interestingly, most of the BVDV-1b strains ( n = 9) identified in brain samples were confirmed by all 3 diagnostic tests. Further studies should be performed to determine why the BVDV-1b strain was found in brain samples that were positive using all 3 diagnostic tests.

Clinical appearance and pathology of cattle persistently infected with bovine viral diarrhoea virus of different genetic subgroups

Bovine viral diarrhoea (BVD) is an economically important cattle disease with a world-wide distribution that is caused by BVD virus, a pestivirus of the flaviviridae family. BVD viruses are genetically highly variable. They are classified into two genetic species (BVDV-1 and -2) that are further divided into numerous subgroups, particularly for BVDV-1. The complexity of these viruses is also reflected in their interaction with the host animals. Infections are either transient or persistent and can cause a wide spectrum of clinical signs, from no or very mild disease to severe forms, reminiscent of viral haemorrhagic fevers. In this work, we have analysed the clinical signs and the pathology of BVD viral infections in a cattle population where different subgroups of BVDV-1 genotype viruses are endemic. In addition, we have examined potential virulence properties of BVDV-1 subgroups during persistent infection by comparing the viral subgroups present in clinical cases with those detected in persistently infected (PI) animals sampled for epidemiological criteria, irrespective of their health condition. Furthermore, the clinical and postmortem findings were compared with respect to genetic characteristics of the viruses isolated from these animals. Our results indicate that the BVDV positive animals fall roughly into two categories, depending on the primary organ affected and the age, with lung-centred pathology occurring mainly in young animals and mucosal pathology predominantly in older animals. Furthermore, we found a markedly higher proportion of representatives of the BVDV-1e subgroup in stillborn calves and aborted foetuses originating from epidemically unrelated cattle herds, suggesting that BVDV-1e may play a special role in prenatal and perinatal losses.

Bovine leukemia virus can be classified into seven genotypes: evidence for the existence of two novel clades

Previous studies have classified the env sequences of bovine leukemia virus (BLV) provirus from different locations worldwide into between two and four genetic groupings. These different studies gave unique names to the identified groups and no study has yet integrated all the available sequences. Thus, we hypothesized that many of the different groups previously identified actually correspond to a limited group of genotypes that are unevenly distributed worldwide. To examine this hypothesis, we sequenced the env gene from 28 BLV field strains and compared these sequences to 46 env sequences that represent all the genetic groupings already identified. By using phylogenetic analyses, we recovered six clades, or genotypes, that we have called genotypes 1, 2, 3, 4, 5 and 6. Genotypes 1–5 have counterparts among the sequence groupings identified previously. One env sequence did not cluster with any of the others and was highly divergent when compared with the six genotypes identified here. Thus, an extra genotype, which we named 7, may exist. Similarity comparisons were highly congruent with phylogenetic analyses. Furthermore, our analyses confirmed the existence of geographical clusters.

Congenital tremor and hypomyelination associated with bovine viral diarrhoea virus in 23 British cattle herds

This paper presents data from 23 British herds investigated between 1991 and 2007 where neurological disease in calves was caused by bovine viral diarrhoea virus (BVDV) infection. A variety of clinical signs, most commonly tremor or trembling, were apparent in the calves from birth, and most were recumbent or unable to stand unsupported. Severe diffuse neuraxial hypomyelination was present in all of the calves, and immunohistochemistry revealed cerebral neuronal labelling consistent with congenital persistent pestivirus infection in each brain. BVDV was detected in peripheral blood samples from eight of 15 calves tested using an antigen ELISA, and was isolated in culture from samples of viscera, brain or blood collected from 17 of 24 affected calves. TaqMan RT-PCR for pestivirus RNA was positive for BVDV-1 in all six calves tested. Six of the virus isolates on which molecular classification was carried out, obtained from calves in four of the herds, were identified as BVDV-1a, while three isolates from one affected and two unaffected calves on a fifth farm were confirmed as BVDV-1b.

Identification of new genetic subtypes of bovine viral diarrhea virus genotype 1 isolated in Japan

A part of the nucleotide sequence of the 5' untranslated region (5'UTR) and E rns region, and the genomic regions encoding for N pro, Core, and E2 of So-like isolates and IS25CP/01 strain which belong to bovine viral diarrhea virus genotype 1 (BVDV-1) were determined and genetic comparisons were made with sequences of other BVDV subgenotypes. Phylogenetic analysis using the 5'UTR and N pro revealed that So-like isolates and IS25CP/01 branched into independent phylogenetic branch. So-like isolates were clustered with Korean BVDV strains taken from DDBL/EMBL/GenBank in the 5'UTR. An additional two amino acid residues were found at the C terminal of the Core region of IS25CP/01. The similarity of amino acid sequence of E2 of So-like isolates and IS25CP/01 to the BVDV-1 reference strain NADL were 78.0-78.5 and 79.0, respectively. Cross-neutralization tests showed significant antigenic differences between So-like isolates and the others (Antigenic similarity (R) value: 2.2-8.8), and IS25CP/01 and the others (R value: 1.6-8.8). So-like viruses and IS25CP/01 differed from the thirteenth subgenotypes (1a-1m) reported by Jackova et al. (2007) and were classified as new genetic subtypes, BVDV-1n (So-like) and 1o (IS25CP/01).

Molecular phylogenetic analysis of bovine viral diarrhoea virus: A Bayesian approach

Genetic typing of bovine viral diarrhoea virus (BVDV) is important for precise classification of viruses. Traditionally, inferring BVDV phylogeny has been performed by distance-based method, i.e. neighbor-joining for single genes. In this study, a Bayesian approach was exploited to analyze five genetic regions of BVDV genome (5' UTR, N(pro), E2a, E2b, and NS3) for 68 taxa retrieved from GenBank. The results showed that all taxa in the consensus tree of E2a have been assigned correctly to corresponding groups, i.e. type-2 BVDV, and BVDV-1a, -1b, -1c, -1e, and -1g, supported by a high posterior probability. In contrast, subgroup 1a formed polytomies in the consensus trees of 5' UTR and NS3. Polytomies also appeared among the subgroup 1b in the consensus trees of N(pro) and E2b. Analysis of a combined dataset produced an unambiguous, well-supported phylogenetic hypothesis. The topologies found for each genetic region separately and combined were different, but the differences were mainly weakly supported by the data. Combining the data allowed the identification of well-supported clades of strains that correspond to some of the previously defined subgroups. Only a combined approach will allow the confident placement of new strains in the current classification of viruses into genotype and subgenotype.

Observations on rinderpest and rinderpest-like diseases throughout West and Central African countries during rinderpest eradication projects

Between 1998 and 2005, the Regional Reference Laboratory at Bingerville (Ivory-Coast) received samples for analysis from Western and Central African countries. From a total of 606 sera; 65 tissue samples and 75 swabs received, no rinderpest virus or specific gene products or antibodies against rinderpest were detected. Use of the PCR on the tissue and swabs (total of 140 samples) identified the genomic presence of BVD (4/140), MCF (2/140), IBR (1/140) and FMD (6/140) viruses. These cause diseases that produce similar clinical signs to rinderpest. The quality of many samples sent to the reference laboratory did not meet the laboratory requirements and this compromised analysis of some specimens.

Genetic characterization of Brazilian bovine viral diarrhea virus isolates by partial nucleotide sequencing of the 5'-UTR region

Nineteen isolates of bovine viral diarrhea virus (BVDV) from Brazil were genetically characterized through partial nucleotide sequencing and analysis of the 5'UTR region. The isolates were grouped as BVDV-1 (11/19), BVDV-2 (6/19) or "atypical" pestivirus (2/19). Among the BVDV-1, eight isolates were classified as subgenotype BVDV-1a, whereas most (4 out of 6) BVDV-2 belonged to subgenotype 2b. Two isolates from aborted fetuses were not classified into any genetic group, being considered atypical BVDVs. Genetic diversity among Brazilian BVDV isolates may be responsible for vaccination and diag-nostic failure and therefore may influence the control strategies for BVDV infection in the country.

Bovine viral diarrhoea virus (BVDV) subgenotypes in diagnostic laboratory accessions: distribution of BVDV1a, 1b, and 2a subgenotypes

The prevalence of bovine viral diarrhoea virus (BVDV) biotypes and subgenotypes was determined from 131 BVDV positive samples from a diagnostic laboratory. The majority of the isolates were from Oklahoma; however, other states including Kansas, Texas, and Arkansas were represented. These BVDV samples were from submissions of 76 live animals and 55 necropsy samples. There were 131 BVDV samples represented by 117 noncytopathic (NCP), 11 cytopathic (CP) and 3 cases with mixed NCP and CP biotypes. The NCP isolates were more common (P < 0.05) than the CP and NCP/CP combination. The BVDV samples were segregated into three subgenotypes by differential PCR and sequencing of a viral genomic region, 5'-untranslated region (5'-UTR). There were more BVDV1b subgenotypes 60/131 (45.8%) than BVDV1a, 37/131 (28.2%) or BVDV2a, 34/131 (26.0%) (P < 0.05). The organ system involvement included the major categories such as respiratory, digestive, mixed/multiple organs, abortions, and persistent infections (PI). All three BVDV subgenotypes were found in persistently infected (PI) cattle and respiratory diseases, both major requests for BVDV diagnosis. Only one of the 131 viruses was genetically similar to the strains present in U.S. vaccines.

A long distance RT-PCR able to amplify the Pestivirus genome

A method to amplify long genomic regions (up to approximately 12.3 kb) from pestiviruses in one RT-PCR is described. The difficulty in designing conserved Pestivirus primers for the amplification of genomes from highly divergent isolates simply by means of overlapping segments is demonstrated using new bioinformatic tools. An alternative procedure consisting of optimizing the length of the genomic cDNA fragments and their subsequent amplification by polymerase chain reaction (PCR) using a limited set of specific primers is described. The amplification of long DNA fragments from a variety of sources, including genomic, mitochondrial, and viral DNAs as well as cDNA produced by reverse transcription (RT) has been achieved using this methodology, known as long distance PCR. In the case of viruses, it is necessary to obtain viral particles from infected cells prior to RT procedures. This work provides improvements in four steps of long distance RT-PCR (L-RT-PCR): (i) preparation of a viral stock, (ii) preparation of template RNA, (iii) reverse transcription and (iv) amplification of the cDNA by LD-PCR. The usefulness of L-RT-PCR is discussed in the light of current knowledge on pestivirus diversity. The genomic sequence of Singer_Arg reference strain obtained using this method is presented and characterized.

Phylogenetic analysis of Portuguese bovine viral diarrhoea virus

Bovine viral diarrhoea virus (BVDV) infections are an important cause of morbidity and mortality worldwide in dairy and beef cattle. To date, little is know about BVDV genotypes circulating in Portugal. For this purpose, a fragment within the 5'-untranslated region (5'-UTR) from 34 Portuguese field strains of BVDV was amplified by RT-PCR, cloned and sequenced. A maximum-likelihood phylogenetic analysis revealed that most of viruses, originated from cattle from different regions of the country, belong to BVDV type 1 (BVDV-1), genotypes 1b (n = 19), 1a (n = 6), 1d (n = 3) and 1e (n = 3); whereas three viruses clustered in BVDV type 2 (BVDV-2). The results from this study demonstrate that BVDV-lb is the most prevalent genotype and also shows the presence of BVDV-2 in Portugal.

Practical significance of heterogeneity among BVDV strains: Impact of biotype and genotype on U.S. control programs

In the early 1990s research groups in North America noted that a newly recognized severe acute form of bovine viral diarrhea virus infection, referred to as hemorrhagic syndrome or severe acute BVDV (SA BVDV), was associated with a genetically distinct subgroup of BVDV strains. This new subgroup was named BVDV genotype 2 or BVDV2. All BVDV strains previously characterized in the literature belonged to a separate genotype, BVDV1. However, not all strains identified as BVDV2 were associated with severe acute infections. If I did this deletion, I did not mean to do it. I think it was already here, though. I see there are some other big edits that I did not do; fine. Hollis subsequent surveys of BVDV strains isolated from clinical submissions to diagnostic laboratories and contaminated fetal calf serum suggested that the ratio of BVDV2 to BVDV1 strains in the U.S. approached 50%. Further, while antigenic cross reactivity is seen between BVDV1 and BVDV2 strains, a log or more difference is typically observed in titers against viruses from different genotypes. These observations prompted vaccine manufacturers in North America to produce vaccines against BVDV that contained antigens from both BVDV1 and BVDV2 strains. Under experimental conditions, these new vaccines offered improved protection against type 2 strains, however field data are still insufficient to assess their efficacy in practice. The BVDV genotypes may also be segregated into subgenotypes. Two subgenotypes of both BVDV1 (BVDV1a and BVDV1b) and BVDV2 (BVDV2a and BVDV2b) have been reported in North American. BVDV2a predominates with BVDV2b isolation a rare event. In contrast, BVDV1a and BVDV1b are both commonly isolated. Antigenic differences observed between strains from the BVDV1a and BVDV1b subgenotypes have led to the suggestion that protection may be improved by inclusion of strains from both BVDV1a and BVDV1b in vaccines in addition to BVDV2. The cost to benefit ratio of this proposal is currently a matter of debate.

Genetic diversity of BVDV: consequences for classification and molecular epidemiology

Genetic typing of bovine viral diarrhoea virus (BVDV) is important for the precise classification of viruses as well as for the development of molecular epidemiology. BVDV isolates were usually typed based on comparison of genomic sequences from the 5'-untranslated region (5'-UTR), N(pro) and E2 region. Recently we have identified 11 genetic groups (subgenotypes) of BVDV-1. Our further experiments confirmed a new subgenotype, BVDV-1k, isolated from cattle in Switzerland. BVDV isolates from India were typed as BVDV-1b whereas BVDV-1c is a predominant subgenotype in Australia. The results of genetic typing of BVDV indicate that distribution of subgenotypes has no relationship to the geographic origin of viral isolates.

BVDV and BHV-1 infections in dairy herds in northern and northeastern Thailand

Bulk milk samples from 220 dairy herds were collected at 9 public milk collection centres in the northeastern and northern Thailand, and a subset of 11 herds was selected for individual testing. The samples were tested for presence of antibodies to BVDV and BHV-1 using an indirect ELISA. The results from the bulk milk testing demonstrated a moderate level of exposure to BVDV and BHV-1 (73% and 67%, respectively). However, the low proportion of herds with high BVDV antibody-levels (13%) and the low within-herd seroprevalence of BVDV and BHV-1 in the 11 herds (24% and 5%, respectively), particularly among the young stock (15% and 0%, respectively), demonstrated a low prevalence of active BVDV infection and a low rate of reactivation of latent BHV-1. The presence of a self-clearance process was also indicated by the results from the individual testing. Moreover, a surprisingly low prevalence of BVDV and BHV-1 antibody-positive herds at one of the milk centres was found. This centre was established 5–10 years before the others. Our impression is that this reflects the self-clearance process, where consecutive replacement of imported infected animals without further spread has resulted in a nearly total elimination of the infections.

Based on our experiences and on these results we are convinced that this process can continue if there is awareness of herd biosecurity. This is especially important in the context of a future intensification of the dairy production.

Homologous recombination in bovine pestiviruses. Phylogenetic and statistic evidence

Bovine pestiviruses (Bovine Viral Diarrea Virus 1 (BVDV 1) and Bovine Viral Diarrea Virus 2 (BVDV 2)) belong to the genus Pestivirus (Flaviviridae), which is composed of positive stranded RNA viruses causing significant economic losses world-wide. We used phylogenetic and bootstrap analyses to systematically scan alignments of previously sequenced genomes in order to explore further the evolutionary mechanisms responsible for variation in the virus. Previously published data suggested that homologous crossover might be one of the mechanisms responsible for the genomic rearrangements observed in cytopathic (cp) strains of bovine pestiviruses. Nevertheless, homologous recombination involves not just homologous crossovers, but also replacement of a homologous region of the acceptor RNA. Furthermore, cytopathic strains represent dead paths in evolution, since they are isolated exclusively from the fatal cases of mucosal disease. Herein, we report evidence of homologous inter-genotype recombination in the genome of a non-cytopathic (ncp) strain of Bovine Viral Diarrea Virus 1, the type species of the genus Pestivirus. We also show that intra-genotype homologous recombination might be a common phenomenon in both species of Pestivirus. This evidence demonstrates that homologous recombination contribute to the diversification of bovine pestiviruses in nature. Implications for virus evolution, taxonomy and phylogenetics are discussed.

Genetic typing of bovine viral diarrhoea virus: most Slovenian isolates are of genotypes 1d and 1f

A selection of 43 bovine viral diarrhoea viruses isolated from mainly persistently infected cattle on 23 Slovenian farms between 1997 and 2001 were characterised genetically. Viral RNA was extracted from infected cell cultures, reverse transcribed and amplified by PCR with primers targeting the 5'-UTR and the N(pro) gene, followed by direct sequencing of purified PCR products obtained for both genomic regions. The N(pro) sequences provided the best genetic resolution, and gave also higher statistical support for phylogenetic classification of the viruses. Thirty-eight of the Slovenian isolates were of genetic subtypes 1d and 1f, four were 1b, and one subtype 1g. No BVDV type 2 viruses were found. This genetic prevalence matched those previously reported for neighbouring countries, as opposed to findings reported for more distant European countries, e.g. France, Spain and the UK. From eight cattle herds several virus isolates were analysed; with one exception all isolates from each herd were of the same genetic group. Extended sequencing of the N(pro) and part of the C gene of virus isolates with identical 5'-UTR sequences allowed differentiation between isolates obtained at different times from one herd.

Phylogenetic analysis of bovine viral diarrhea viruses using five different genetic regions

Phylogenetic analysis of the five different regions (5' non-coding region (5'NCR), N(pro), E2, NS3 and NS5B-3'NCR) of 48 Japanese and reported bovine viral diarrhea virus (BVDV) genomes was performed. Japanese BVDVs were segregated into BVDV1 subdivided into six subgroups and BVDV2. One isolate, So CP/75, isolated in 1975 and previously proposed as subgroup 1e according to its 5'NCR sequence, was quite unique and formed an independent lineage in the tree of any region. Another isolate, 190CP, obtained from an experimental mucosal disease case was classified as subgroup 1e, defined by Becher et al. in the 5'NCR, N(pro) and E2 regions, whereas it was classified as subgroup 1a in the NS5B-3'NCR region. The genomic sequences of the American isolates ILLC and ILLNC obtained from the GenBank database were assigned into subgroup 1b in the 5'NCR, N(pro), E2 and NS5B-3'NCR regions, whereas they were assigned into subgroup 1a in the NS3 region, suggesting that recombination between the virus strains classified into different subgroups had occurred in an animal. These findings suggest that phylogenetic analysis of several genetic regions is useful for the further characterization of field BVDV isolates.

Bovine viral diarrhea virus 1 is classified into different subgenotypes depending on the analyzed region within the viral genome

Phylogenetic analyses of bovine viral diarrhea virus (BVDV) were performed based on the nucleotide sequences of the 5' untranslated region (5'-UTR) and E2-coding gene. Thirty-six BVDV detected from naturally infected cattle in the northern region of Japan were divided into three genotypes, BVDV1a, BVDV1b and BVDV2, in a 5'-UTR phylogenetic tree. In a phylogenetic tree constructed from the E2-coding gene, BVDV1c was identified and the viruses classified in BVDV1c were included in BVDV1a in the 5'-UTR phylogenetic tree. Moreover, BVDV1a and BVDV1b in the E2-phylogenetic tree clustered closer together than in the 5'-UTR tree. These results suggested that phylogenetic analysis of the E2 gene was more useful for identification of subgenotypes within BVDV1.

Emergence of a novel subgroup within the widely circulating lineage of foot-and-mouth disease virus serotype Asia 1 in India

The complete VP1 encoding (1D) gene of 54 foot-and-mouth disease (FMD) virus serotype Asia1 field isolates, most of which were isolated during 2000 and 2001, was sequenced. The phylogenetic analysis identified a novel subgroup (>10% nucleotide divergence) within the widely circulating lineage of this serotype. The newly emerged viruses were responsible for disease outbreaks in both cattle and buffaloes and were present in six different states in the country. Amino acid sequence comparison of these isolates revealed significant sequence divergence at many of the amino acid positions in comparison to those of lineage VI-A and C. Emergence of such viruses may affect the efficacy of vaccine strain currently used for protection against FMD in India.

Genetic heterogeneity of bovine viral diarrhoea virus in Italy

The genetic characteristics, of 38 field isolates of bovine viral diarrhoea virus (BVDV) collected in 1999 from sick or healthy and persistently infected cattle of dairy farms situated in northern Italy, were investigated. A partial 5'-untranslated region (5'-UTR) sequence of each isolate was determined and a phylogenetic analysis was performed. All the isolates were classified as belonging to the BVDV-1 genotype and could be assigned to different BVDV-1 groups, namely BVDV-1b (n = 20), BVDV-1d (n = 6) and BVDV-1e (n = 10). Two remaining isolates could be classified as BVDV-1f and BVDV-1h, respectively. These results provided evidence for genetic heterogeneity of BVDV in Italy, and contribute to a better knowledge of the circulation of BVDV strains, and to their classification.

Bovine viral diarrhea virus genomic associations in mucosal disease, enteritis and generalized dermatitis outbreaks in Argentina

The objective of the present work is the description outbreaks caused by bovine viral diarrhea virus (BVDV) in commercial beef cattle ranches in Argentina. Genetic affiliation and their association with the clinical manifestation were carried out with five BVDV isolates from an outbreak of mucosal disease (MD) (Outbreak #1), acute enteritis (Outbreaks #2 and #3) and generalized dermatitis (Outbreaks #4 and #5). Upon genetic analysis CP BVDV isolate of Outbreak #1 clustered to closely to BVDV Oregon (Genotype 1). BVDV isolates from the outbreaks of generalized dermatitis (Outbreaks #4 and #5) were located close to BVDV Osloss within Genotype 1. The identification by immunohistochemistry of BVDV in exudative dermatitis indicates the epithelial cell tropism of the virus. Phylogenic characterization of BVDV from Outbreaks #2 and #3 locate them as BVDV-2. 5'UTR sequence of these viruses revealed a homology of 88 and 90% to BVDV-890 (Genotype 2) and a 77 and 75% to BVDV-SD1 (Genotype 1), respectively. The association of BVDV-2 with severe disease indicates the presence of highly virulent strains. Data from natural outbreaks where BVDV-1 and BVDV-2 were isolated revealed that pathology overlaps and not clearly allows the differentiation between genotypes based on gross or microscopic lesions. Thus, for a definitive diagnosis, further virology and molecular studies are necessary. Additionally, the results of this work focused on the origin and consequences of genetic variations of BVDV with regard to pathogenesis and suggest the association between genotype and a defined clinical syndrome.

Expression of the genomic form of the bovine viral diarrhea virus E2 ORF in a bovine herpesvirus-1 vector

Bovine viral diarrhea virus (BVDV) is a ubiquitous pathogen of cattle with a world-wide distribution. Recently, the possibility of using recombinant virus vectors to immunize cattle against selected BVDV genes has gained widespread interest. Among the virus vectors tested, bovine herpesvirus-1 (BHV1) provides many unique advantages. However, results of recent studies have raised the possibility that the codon usage pattern required for optimal expression in a BHV1-infected cell may be incompatible with the codon usage pattern of BVDV. If true, use of BHV1 to express BVDV proteins would require construction of synthetic BVDV genes that have been modified to resemble the codon pattern of BHV1. To explore this possibility, we constructed a BHV1 recombinant containing the genomic form of the BVDV (NADL) E2 ORF and compared expression of the E2 protein with that of the endogenous BHV1 gD protein. We observed that E2 was expressed at a significant rate compared to that of the gD protein. We conclude that codon usage problems are unlikely to constitute a serious problem for expression of BVDV proteins in BHV1 vectors.

A hepadnavirus regulatory element enhances expression of a type 2 bovine viral diarrhea virus E2 protein from a bovine herpesvirus 1 vector

Recently, the possibility of using virus vectors to immunize cattle against selected bovine viral diarrhea virus (BVDV) genes has gained widespread interest. However, when we attempted to express the E2 protein from type 2 (890 strain) BVDV in a bovine herpesvirus 1 (BHV1) vector, we observed that expression was poor. This often happens when genes from a cytoplasmic virus are expressed in the cell nucleus. To counter this effect, we attempted to enhance expression by a strategy employed by viruses. RNAs of retroviruses and hepadnaviruses contain cis-acting elements that facilitate expression of RNAs that otherwise are degraded or retained within the nucleus. In Mason-Pfizer monkey virus, the required RNA sequence element is known as a constitutive transport element (CTE). A related element from woodchuck hepatitis virus is known as the woodchuck posttranscriptional regulatory element (WPRE). We tested the ability of the CTE, the WPRE, and introns to enhance expression of E2. All three elements stimulated expression of E2 from plasmids. The combination of the WPRE and an intron yielded the highest level of E2 expression in plasmids. However, when E2 was expressed from a BHV1 vector, the presence of an intron was inhibitory. In contrast, the WPRE was very efficient at stimulating E2 expression from a BHV1 vector. This result represents the first expression of a type 2 BVDV E2 protein from a mammalian virus vector and raises the possibility that the WPRE may provide a general method of enhancing foreign gene expression from BHV1 and other herpesvirus vectors.

Genetic diversity of ruminant pestiviruses from Spain

The genetic diversity of ruminant pestiviruses from Spain was investigated by sequencing analysis of the 5' non-coding region (5'NCR) from 10 ovine and 41 bovine samples collected along 4 years (1999-2002) from different farms. The 5'NCR amplicons generated by a one-tube RT-PCR using primers 324/326 were sequenced and phylogenetically analyzed. When compared with strains from GenBank database, Spanish viruses clustered into three genotypes: BVDV 1, BDV and CSFV. No BVDV 2 strains were identified. The 41 bovine samples were all BVDV 1 genotype, but they were further subdivided into subgroups 1b (35) and 1e (6). There was no apparent association between the genotype and clinical symptoms, or the geographic area of origin. However, subgroup 1e has been recently described for isolates from France and, interestingly, subgroup 1e viruses were collected from areas close to the French border. Nine of the ten ovine samples formed a tight cluster within BDV type but clearly differed from BDV subgroups A and B sustaining the need to define a new subgroup as BDV-C in which these ovine strains would be included. Finally, although further studies are needed, the grouping of an ovine sample with CSFV strains would be the first description of a CSFV genotype for ovine pestiviruses.

Genetic diversity of recent bovine viral diarrhoea viruses from the southeast of Austria (Styria)

To characterise the bovine virus diarrhoea virus (BVDV) isolates circulating in the southeastern region of Austria, namely in the province of Styria, 71 blood samples collected between 1998 and 2000 from persistently infected cattle in 62 herds were subjected to genetic typing. For this, 288bp fragments from the 5' untranslated region (5'-UTR) were amplified by polymerase chain reaction after reverse transcription (RT-PCR). The products were sequenced and used for phylogenetic analysis. Seventy virus isolates were typed as BVDV species 1 (BVDV-1). Only one isolate was typed as BVDV species 2 (BVDV-2), representing the first isolate of this pestivirus genotype found in Austria. In addition, phylogenetic analysis revealed that viruses belonging to five genetic groups within BVDV-1 are circulating in Styria. Most viruses (53) were found in group BVDV-1f, nine viruses in BVDV-1h, four viruses in BVDV-1b, three viruses in BVDV-1d and one virus in BVDV-1g. No virus was found in genetic group BVDV-1a, which is dominant in the UK and widely distributed in USA. Likewise, the BVDV isolates predominating in a neighbouring country, namely Germany, belonged to different genogroups than those circulating in Styria. We conclude that in a particular region and environment certain BVDV-1 genetic groups predominate. New groups, including BVDV-2, can be introduced, e.g. by trade of animals. The low incidence of BVDV-2 in Styria is in concert with the sporadic occurrence of these viruses in other regions of Europe.

Isolation of bovine viral diarrhea virus from an alpaca

A frozen, stillborn alpaca (Lama pacos) was submitted to the Minnesota Veterinary Diagnostic Laboratory for diagnostic purposes. No gross or histopathologic changes of any significance were seen. A pool of lung, liver, and brain tissues was positive for bovine viral diarrhea virus (BVDV) by reverse transcription-polymerase chain reaction. On inoculation in cell cultures, a noncytopathic BVDV (type 1b) was isolated. No evidence of BVDV was seen on immunohistochemical examination of tissues. This indicates the importance of using multiple tests for arriving at a diagnosis and appears to be the first report of BVDV isolation from alpaca.

Quasispecies in the 5' untranslated genomic region of bovine viral diarrhoea virus from a single individual

The variability of the 5' untranslated genomic region (5'UTR) of bovine viral diarrhoea virus (BVDV) RNA obtained from a single individual was analysed. Lung, kidney and spleen tissues from a naturally infected foetus were used as the source of viral RNA. A fragment of 288 bases of the internal ribosome entry site from the BVDV 5'UTR was amplified by RT-PCR using a proofreading DNA polymerase. PCR products were cloned into pGem and, subsequently, transformed into Escherichia coli. The single-strand conformational polymorphisms of 158 lung-derived clones were analysed; a total of 11 banding patterns was observed. DNAs corresponding to all patterns were sequenced. Of the randomly selected clones, 11 and 10 clones derived from the kidney and spleen, respectively, were also sequenced. All sequences presented differences ranging from 1 to 6 nt substitutions. Analysis of the secondary structure of the variant sequences and comparisons to variant nucleotide sites from the 5'UTR of several BVDV isolates showed that the observed changes were almost free of randomness. Clustering and phylogenetic analyses suggested the existence of low-kinetic variants. BVDV quasispecies may be involved in establishing persistent infections by means of eluding maternal antibodies. The methods described here may be adapted easily both to analyse large numbers of samples from other genomic regions and for the study of BVDV quasispecies evolution in other systems.

Phylogenetic analysis of the 5'-untranslated region of german BVDV type II isolates

On the basis of genetic differences, bovine viral diarrhoea viruses (BVDV) are subclassified into two distinct genotypes, BVDV type I and BVDV type II. We selected German BVDV type II isolates using the BVDV type I-specific monoclonal antibody WB160 and flow cytometric analysis for further characterization. For molecular characterization, a 288-bp fragment of the 5'-untranslated region (5'-UTR) of the selected isolates was investigated by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing. Sequence comparisons of the partial 5'-UTR sequences and their phylogenetic analyses demonstrated that the 18 German BVDV type II isolates all belong to either subtype IIa (10 isolates) or subtype IIc (eight isolates). Nevertheless, the German BVDV type II isolates were genetically different (89.9-94.3% sequence identity) from the standard BVDV type II strain 890 from North America, which was recently classified as BVDV type IIa. Furthermore, a clear subdivision of the German BVDV type II isolates into two distinct subtypes (BVDV IIa Germany and BVDV IIc Germany) is shown. Viruses of both subgroups differed in the analysed 5'-UTR fragment from each other (91.6-95.2% sequence identity), but were highly conserved within the same German subtype (97.2-100% sequence identity). These findings are discussed in the context of BVDV type II origin, possible introduction into Germany, its epidemiology and impact for vaccine development.

Distribution pattern of bovine viral diarrhoea virus strains in intensive cattle herds in Italy

The genetic variation of bovine viral diarrhoea virus (BVDV) was studied by comparative nucleotide sequence analysis of 26 Italian field strains collected during the period 1995-2000 in 18 cattle herds. A fragment within the 5'-untranslated region (UTR) was sequenced directly from gel-purified products obtained by reverse transcription polymerase chain reaction. BVDV-1b (n=14), -1c (n=1), -1d (n=1) and BVDV-2 (n=2) strains have been isolated. Most herds were infected by BVDV-1b. Pairwise similarity and cluster analysis of the remaining BVDV-1 isolates (n=8) did not provide a clear-cut assignation to defined BVDV-1 groups. This is the first time that a BVDV-2 isolation was reported in Italy. Among BVDV-2 reference strains, Italian BVDV-2 isolates showed the highest sequence similarity with the CD87 strain. Both BVDV-2 strains were isolated in two healthy animals from different herds. The 5'-UTR sequence of one of the two BVDV-2 strains was identical to a German BVDV field strain. Complete nucleotide homology was found only among BVDV strains isolated from the same herd, showing a herd-specific clustering. Moreover, 99.6% homology was observed between strains from herds linked by livestock trade. Despite the small number of BVDV isolates analysed, it revealed a high level of genetic diversity among Italian field BVDV strains.

Prevalence of genotypes 1 and 2 of bovine viral diarrhea virus in Lower Saxony, Germany

The aim of this study was to find whether an antigenic drift had occurred in Lower Saxony in the past 40 years. For this, the genetic diversity of bovine viral diarrhea virus (BVDV) isolates mainly from Lower Saxony was estimated by RT-PCR and sequencing of a 420 bp fragment of the E2 glycoprotein gene. Sixty-one field virus isolates collected during routine diagnostics between 1960 and 2000 in Lower Saxony, Northern Germany, were analyzed. Phylogenetic analysis allowed discrimination of genotypes BVDV 1 and 2. Excepting two isolates, which were of BVDV type 2, most of the isolates were classified as BVDV type 1. This group could be further subdivided into four subgroups and one disparate isolate. Independent of the year of isolation and geographical localization, 54 isolates clustered in two subtypes (BVDV subtypes 1b and 1d). Only one isolate was classified as BVDV type 1a, thus being similar to the North American NADL strain, and to the vaccine strain Oregon C24V, which was extensively used for vaccination in Germany. The remaining isolates belonged to new clusters tentatively designated as BVDV subtypes 1g and 1f. To compare the cluster designation with that of other studies, phylogenetic analysis of representatives of each of the subgroups based on the 5' untranslated region (5'UTR) was performed. It grouped the viruses similarly. The results indicate that the BVDV population seems to be relatively stable over 40 years in Lower Saxony.