Relationships amongst bluetongue viruses revealed by comparisons of capsid and outer coat protein nucleotide sequences

Phylogenetic comparison of the S3 gene of United States prototype strains of bluetongue virus with that of field isolates from California

To better define the molecular epidemiology of bluetongue virus (BTV) infection, the genetic characteristics and phylogenetic relationships of the S3 genes of the five U.S. prototype strains of BTV, the commercially available serotype 10 modified live virus vaccine, and 18 field isolates of BTV serotypes 10, 11, 13, and 17 obtained in California during 1980, 1981, 1989, and 1990 were determined. With the exception of the S3 gene of the U.S. prototype strain of BTV serotype 2 (BTV 2), these viruses had an overall sequence homology of between 95 and 100%. Phylogenetic analyses segregated the prototype U.S. BTV 2 strain to a unique branch (100% bootstrap value), whereas the rest of the viruses clustered in two main monophyletic groups that were not correlated with their serotype, year of isolation, or geographical origin. The lack of consistent association between S3 gene sequence and virus serotype likely is a consequence of reassortment of BTV gene segments during natural mixed infections of vertebrate and invertebrate hosts. The prototype strain of BTV 13, which is considered an introduction to the U.S. like BTV 2, presents an S3 gene which is highly homologous to those of some isolates of BTV 10 and especially to that of the vaccine strain. This finding strongly suggests that the U.S. prototype strain of BTV 13 is a natural reassortant. The different topologies of the phylogenetic trees of the L2 and S3 genes of the various viruses indicate that these two genome segments evolve independently. We conclude that the S3 gene segment of populations of BTV in California is formed by different consensus sequences which cocirculate and which cannot be grouped by serotype.

Phylogenetic comparison of the serotype-specific VP2 protein of bluetongue and related orbiviruses

Regions of the VP2 gene from various bluetongue virus serotypes were sequenced and phylogenetic comparisons were performed. The sequences were characteristic for each BTV serotype and isolates of the same serotype could be grouped geographically, mimicking the topotyping characteristics of BTV VP3 gene sequences. PCR amplification and sequence analysis were used to show the close relationship between Caribbean BTV isolates and South African BTV isolates of the same serotype. Similarly, Australian BTV isolates showed a close genetic relationship with Asian BTV isolates of the same serotype. A multiple amino acid sequence alignment of fifteen BTV serotypes and other orbiviruses over a proposed major neutralization site showed this region (317 335 aa.) was highly variable and nucleotide sequences showed that BTV serotypes could be grouped into nucleotypes, or related serotypes, in broad agreement with the inter-relationships postulated by Erasmus (1990), using plaque-reduction tests.

Identification of the major North American bluetongue viruses using nucleic acid amplification techniques

A set of primers (BTV-pr1/2) were selected that hybridized to the VP3 gene of the major North American serotypes of bluetongue virus (BTV). Polymerase chain reaction (PCR) testing yielded positive results from specimens of major North American BTV isolates (serotypes 10, 11, 13 and 17) propagated in Vero cells. In addition, PCR assays were positive from samples of all other BTV serotypes, except BTV-16; however, an alternative primer pair (BTV-prN1/N2) was devised for amplification of this serotype and the major North American BTV serotypes. PCR products were not evident following amplification of related viruses, epizootic haemorrhagic disease virus (EHDV) serotypes 1 or 2, in either PCR test. In addition, slight modification of the nucleic acid extraction method allowed for the amplification of BTV template from ovine and cervine blood, but not from the respective control blood samples. Restriction endonuclease analysis (REA) using AluI and TaqI discriminated the PCR products of BTV serotypes 10, 13 and 11/17. Identification of BTV-11 and -17 was accomplished by PCR product nucleotide sequencing. Thus, using a single gene region (VP3), nucleic acid amplification methods were devised for expeditious serogroup-specific detection of all BTV serotypes and identification of individual North American BTV nucleotypes, which is expected to prove valuable for disease control strategies and retrospective epidemiological analyses.

Geographical genetic variation in the gene encoding VP3 from the Alberta isolate of epizootic hemorrhagic disease virus

The complete nucleic acid and deduced amino acid sequences of gene segment 3 and the encoded VP3 from the North American, Alberta isolate of epizootic hemorrhagic disease virus serotype 2 (EHDV-2) are reported. Complementary DNA corresponding to segment 3 was 2768 nucleotides in length with an open reading frame of 2697 base pairs which encoded a VP3 polypeptide of 899 amino acid residues. Sequence comparison with genome segment 3 and VP3 from the Australian strain of EHDV-2 indicated genotypic and phenotypic homologies of 79% and 94%, respectively. Two North American field isolates of EHDV-2, as well as EHDV-1 (New Jersey isolate), had virtually identical homology to the Alberta isolate. Sequence analysis delineated North American EHDV strains as members of a genetically homologous and geographically distinct group of orbiviruses (topotype). The data support the hypothesis that geographic isolation between North American and Australian orbiviruses has permitted the viral topotypes to maintain their genetic distinctness.

Complete nucleotide sequence of RNA segment 3 of bluetongue virus serotype 2 (Ona-A). Phylogenetic analyses reveal the probable origin and relationship with other orbiviruses

The nucleotide sequence of the RNA segment 3 of bluetongue virus (BTV) serotype 2 (Ona-A) from North America was determined to be 2772 nucleotides containing a single large open reading frame of 2703 nucleotides (901 amino acid). The predicted VP3 protein exhibited general physiochemical properties (including hydropathy profiles) which were very similar to those previously deduced for other BTV VP3 proteins. Partial genome segment 3 sequences, obtained by polymerase chain reaction (PCR) sequencing, of BTV isolates from the Caribbean were compared to those from North America, South Africa, India, Indonesia, Malaysia and Australia, as well as other orbiviruses, to determine the phylogenetic relationships amongst them. Three major BTV topotypes (Gould, A.R. (1987) Virus Res. 7, 169-183) were observed which had nucleotide sequences that differed by approximately 20%. At the molecular level, geographic separation had resulted in significant divergence in the BTV genome segment 3 sequences, consistent with the evolution of distinct viral populations. The close phylogenetic relationship between the BTV serotype 2 (Ona-A strain) from Florida and the BTV serotypes 1, 6 and 12 from Jamaica and Honduras, indicated that the presence of BTV serotype 2 in North America was probably due to an exotic incursion from the Caribbean region as previously proposed by Sellers and Maaroof ((1989) Can. J. Vet. Res. 53, 100-102) based on trajectory analysis. Conversely, nucleotide sequence analysis of Caribbean BTV serotype 17 isolates suggested they arose from incursions which originated in the USA, possibly from a BTV population distinct from those circulating in Wyoming.

Phylogenetic relationships of the VP2 protein of a virulent isolate of bluetongue virus (BTV-23) compared to those of 6 other BTV serotypes

To determine the genetic relationship of the virulent Australian bluetongue virus serotype 23 with that of other serotypes and to identify the extent and nature of the antigenic variation among seven serotypes of bluetongue virus (BTV), the complete nucleotide sequence was determined for cDNA clones representing the L2 dsRNA of BTV-23, the gene that codes for the outer capsid neutralization antigen (VP2). The predicted amino acid sequence of the protein was compared with the VP2 sequences of the five USA serotypes (BTV-2, -10, -11, -13 and -17) as well as with an Australian isolate of BTV-1. The comparisons revealed that the VP2 of BTV-23 is most closely related to that of BTV-1, sharing 52% identical and 72% similar sequences, also that the VP2 of the two Australian serotypes are more closely related to that of BTV-2 than to the other four USA serotypes. Only 22% identical sequences are shared by all seven VP2 molecules; however, when homologous substitutions are considered the similarity index was as high as 48%. In addition, the conserved regions that have been identified previously for other VP2 molecules are also conserved in BTV-23.

The orbivirus genus. Diversity, structure, replication and phylogenetic relationships

The general properties of the orbiviruses have been examined at the physical, structural and molecular level. At the structural level, the orbiviruses (with the exception of the Kemerovo serogroup) appear similar. The replicative events are also similar, however differences in the ultrastructure of virus-specific structures and their association with components of the host cell have been observed. Further research in this area may be used to differentiate between the serogroups and even some serotypes, of orbiviruses. At the molecular level the properties of the genome can be used to determine relationships between members of the orbivirus genus. These relationships are revealed using a variety of techniques including serology and gene sequence analysis. Not only are the different serological responses to gene products present in the mature virus particle used for differential diagnosis, but the gene sequences themselves can also be utilized. Understanding of the relationships between these viruses is progressing to the point that insights into orbivirus molecular epidemiology is now possible.

A rapid indirect ELISA for the serogrouping of Australian orbiviruses

This communication describes the development and evaluation of a simple and rapid method for the classification of Australian orbiviruses into one of seven established serogroups (i.e. bluetongue, epizootic haemorrhagic disease of deer, Palyam, Eubenangee, Corriparta, Wallal, Warrego) or an 'ungrouped' category. The Australian orbivirus serogrouping ELISA (SG-ELISA) utilised a sodium deoxycholate-treated cell lysate preparation from infected BHK cells which was subsequently probed in an indirect ELISA format with polyclonal antibodies representative of each serogroup. Bound immunoglobulin was detected by the use of a recombinant streptococcal protein G-HRPO conjugate and subsequent reaction with the chromogenic substrate. All reference orbiviruses tested in the SG-ELISA were identified and were in agreement with the serogroups originally designated. Minimal inter-serogroup cross-reactions were observed. One-way cross-reactions were observed between Warrego and Mitchell River viruses.

The pathogenesis and immunology of bluetongue virus infection of ruminants

Bluetongue (BLU) virus is transmitted from infected to susceptible ruminants by hematophagous vector midges (Culicoides species). Cattle are important reservoir hosts of the virus because infection typically is asymptomatic and characterized by prolonged cell associated viremia, and because at least some species of insect vector preferentially feed on cattle. Interaction of BLU virus with the cell membrane of erythrocytes in infected cattle likely facilitates both prolonged viremia as well as infection of the insect vector. BLU disease is most common in sheep and some wildlife species. A variety of host, agent and environmental factors clearly can influence expression of disease in these species. The pathogenesis of BLU virus infection of cattle and sheep is remarkably similar, thus the basis for expression of disease in sheep but not cattle remains to be firmly established. Some difference in susceptibility of endothelial cells to infection in the two species is one potential explanation. Ruminants develop a variety of antiviral responses after BLU virus infection. Antibodies to outer capsid protein VP2 are responsible for virus neutralization, and confer resistance to reinfection with the homologous serotype of BLU virus. Antibodies to epitopes on proteins which are common to all viruses of the BLU serogroup form the basis of current diagnostic serologic tests. Cell mediated responses have been incompletely characterized, in part because BLU virus replicates within dividing lymphocytes and virus-mediated cytolysis inhibits in vitro blastogenesis. Immunological competence of ruminants to BLU virus arises prior to midgestation, and suggestions that persistent immune tolerant BLU virus infection occurs after in utero exposure of cattle have not been substantiated and are not consistent with recent findings.

Phylogenetic characterisation of bluetongue viruses from naturally-infected insects, cattle and sheep in Australia

The polymerase chain reaction was used to detect the presence of bluetongue virus (BTV) in a number of clinical and insect samples collected in the Northern Territory of Australia. Sequence analyses of the amplified BTV genes differentiated endemic Australian and exotic viruses. Two potential exotic BTV were detected as a result of PCR analyses of blood from sentinel animals and of the insect vector, Culicoides wadai. The detection of BTV in C wadai was the first direct demonstration of the presence of BTV in this potential vector. This new technology can significantly reduce the time taken for a diagnosis from a clinical sample and increase the amount of useful information obtained on a BTV isolate by using rapid sequencing techniques. Sequence data were used to differentiate between BTV20 isolated in 1975 and two isolates of the same serotype, isolated in 1992, and indicated that the latter were probably a recent incursion into Australia from Indonesia due to their greater VP3 sequence homology to the BTV9 (Java) than to Australian BTV isolates.

Heterogeneity of the L2 gene of field isolates of bluetongue virus serotype 17 from the San Joaquin Valley of California

Genome segment 2 (L2) from six field isolates of bluetongue virus (BTV) serotype 17 was sequenced by cycling sequencing after the amplification of the viral cDNA by the polymerase chain reaction. The viruses were isolated from sheep, cattle and a goat in the San Joaquin Valley of California during the years 1981 and 1990. These viruses exhibit divergent patterns of neutralization with BTV 17-specific monoclonal antibodies. The six L2 genes of the BTV 17 field isolates all encode a protein of 955 amino acids. Similarity of the nucleotide sequences of the L2 genes with respect to the prototype strain ranges between 93.8% and 95.1%, whereas the similarity between the field isolates ranges from 96.8% to 99.1%. Although very closely related, the L2 gene of each virus is distinct. Furthermore, mutations in the L2 gene of field isolates of BTV do not consistently follow a linear pattern of accumulation over time. Some amino acid changes in the VP2 protein of field strains were conserved over time, whereas others were not correlated with the year of isolation and some substitutions were unique to individual viruses. The predicted VP2s constitute a group of non-identical, but closely related proteins. Phylogenetic analyses suggest that the viral variants which co-circulate in the San Joaquin Valley could evolve by different evolutionary pathways.

Polymerase chain reaction and other laboratory techniques in the diagnosis of long incubation rabies in Australia

Blood and post-mortem tissues from a 10-years-old girl were submitted to the Australian Animal Health Laboratory. Clinical signs and histopathological lesions had suggested a diagnosis of rabies, but, an unusually long incubation period of at least 5 years did not encourage such a diagnosis. Serological examinations by the rapid fluorescent focus inhibition test revealed a dramatic increase in rabies virus-neutralising antibody during the 10-day period of hospitalisation. The results of a fluorescent antibody test on brain smears, and an immunoperoxidase test on formalin-fixed sections of brain were also consistent with a diagnosis of rabies. Attempts to isolate virus were unsuccessful. Polymerase chain reactions (PCRs) were conducted on a 10% suspension of a post-mortem sample from the patient's brain, using primers based on the published sequence of the Pasteur virus strain of rabies virus. 413 and 513 bp fragments from the nucleoprotein gene and a 403 bp fragment from the glycoprotein gene were amplified. Subsequent sequencing of these fragments, and comparison with equivalent regions of known rabies viruses, confirmed that the fragments originated from a virus belonging to the rabies virus serotype. This case demonstrated the advantage of using a range of laboratory techniques to obtain a definitive diagnosis. In particular, a PCR-based test may allow a diagnosis, even in the face of conditions that preclude virus isolation such as apparently occurred in this case. Finally, this case demonstrated that an unusually long incubation period should not discourage a tentative clinical diagnosis of rabies.

Genetic variation and evolutionary relationships amongst bluetongue viruses endemic in the United States

The genetic variation and evolutionary relationships amongst the five serotypes of bluetongue virus (BTV) endemic to the United States were investigated by oligonucleotide fingerprint analysis. The viruses analyzed include prototype viruses of the five U.S. serotypes, and 32 viruses isolated from domestic and wild ruminants from the U.S. in the years 1979-1981. With the exception of serotype 2, most genes encoding the viral core and non-structural proteins were demonstrated to be highly conserved both within and between serotypes and some also appear to have reassorted in nature. Gene segments 2 and 6, which encode the outer capsid proteins VP2 and VP5 respectively, were more variable and were not consistently linked as serotype determination was dependent solely on gene segment 2. Gene segment 2 was the most variable gene between serotypes, but it was highly conserved within serotypes and stable over time. This suggests that the emergence of new BTV serotypes, which would require the stable incorporation of numerous mutations, must be a very slow process. Fingerprint comparisons further suggested that BTV serotypes 10, 11, 13 and 17 have evolved together in the U.S. over a considerable period of time, whereas serotype 2, which is genetically distinct, has evolved elsewhere and is most likely a recent introduction to North America.

Phylogenetic analyses of the complete nucleotide sequence of the capsid protein (VP3) of Australian epizootic haemorrhagic disease of deer virus (serotype 2) and cognate genes from other orbiviruses

The complete nucleotide sequence of the minor capsid protein (VP3) of epizootic haemorrhagic disease of deer virus (EHDV; Australian serotype 2) was determined using a combination of cloning and sequencing methods. Gene segment 3 that coded for the EHDV VP3 capsid protein was 2768 nucleotides in length with a coding region of 2697 nucleotides flanked by 5' and 3' non-coding regions of 17 and 53 nucleotides, respectively. A protein of 899 amino acids (Mr 103,160) having no overall charge at neutral pH was deduced from the nucleotide sequence. Comparisons with equivalent regions from the other Australian EHDV serotypes showed the VP3 genes and the segments that coded for them were similar, varying by a maximum of 5%. Comparisons with known cognate genes from bluetongue viruses showed that their VP3 genes and the proteins translated from them were remarkably similar to those of EHDV, having approximately 70% to 80% homology at either level, respectively. In an attempt to delineate the evolution of orbiviruses, we have obtained sequence data from the VP3 genes from representative members of all Australian orbiviruses now known. Computer analyses of this data enabled a phylogenetic tree for the orbiviruses to be proposed that incorporated the concept of topotypes.

Detection and characterisation of bluetongue virus using the polymerase chain reaction

Pairs of oligodeoxynucleotide primers whose sequences were based on those of RNA segment 3 that encodes the bluetongue virus serogroup-reactive protein VP3, were synthesized for three BTVs from different geographic regions of the world and for seven Australian orbiviruses. Each pair of primers was then tested for the synthesis of cDNA and in subsequent polymerase chain reactions (PCR) with all ten virus groups. All primers were serogroup-specific at low or high stringency. One pair of primers was specifically designed for its ability to serogroup a BTV isolate irrespective of its geographic origin. At either high or low stringency, this primer-pair resulted in a common and specific PCR product for each of the BTVs tested but not for the other orbiviruses. Eight pairs of primers based on RNA2 sequences (the gene segment encoding the serotype-specific protein VP2) were also synthesized for the eight Australian serotypes of BTV. Each primer-pair was serotype-specific at low or high stringency except for the BTV16A pair, which cross-reacted with BTV3A and also gave a non-specific product that differed in Mr from the authentic PCR product. Using the PCR and BTV1A RNA3-based primers, BTV1A was detected in blood samples from two sheep at 9 days post inoculation. Virus was found in the platelet, buffy-coat and packed red blood cell fractions, but not in whole blood.

The amino acid sequence of the outer coat protein VP2 of neutralizing monoclonal antibody-resistant, virulent and attenuated bluetongue viruses

Monoclonal antibodies which reacted with four different epitopes were used to select neutralization-resistant variants of Australian bluetongue virus serotype 1 (BTV1AUS; isolate CS156). Nucleotide sequencing of the VP2 outer coat protein gene of these variants showed that two of them contained alterations within the previously defined neutralization site at amino acids 328 to 335 (Gould et al., 1988). Comparison of VP2 sequences of several BTV serotypes, in addition to nucleotide sequence changes in a number of variants, suggested that this neutralization site was larger and contained 19 amino acids, the conformation of which could be affected by other regions of the VP2 protein. Nucleotide sequencing of neutralization-resistant variants revealed a total of four other regions of VP2 affecting the ability of monoclonal antibodies to neutralize the virus and these results support the notion that the neutralization site in VP2 was conformation dependent. The complete nucleotide sequence of the VP2 gene of virulent BTV1AUS (C5156) was determined directly from viral nucleic acid isolated from the blood of a sheep suffering clinical bluetongue disease. Comparison of the VP2 sequence of this virulent virus with that previously published for an avirulent, laboratory strain (Gould, 1988), indicated that the passage of virulent virus approximately 20 times in tissue culture over the last decade, not only led to attenuation but resulted in the appearance of ten nucleotide changes in the VP2 gene. Six of these nucleotide changes were silent, two resulted in conservative amino acid substitutions and two generated radical amino acid changes. However, in a separate experiment, a single passage of the virulent virus in tissue culture while leading to attenuation did not result in a nucleotide change in the VP2 outer coat protein gene.