Phylogenetic analysis of the S10 gene of field and laboratory strains of bluetongue virus from the United States

Recent US bluetongue virus serotype 3 isolates found outside of Florida indicate evidence of reassortment with co-circulating endemic serotypes

Since 1999, 11 serotypes of bluetongue virus (BTV) similar to Central American or Caribbean strains have been isolated in the southeastern United States, predominantly in Florida. The majority of the incursive serotypes have remained restricted to the southeastern US. In recent years, BTV serotype 3 (BTV-3) has been isolated in areas increasingly distant from Florida. The current study uses whole genome sequencing of recent and historical BTV-3 isolates from the US, Central America and the Caribbean with additional sequences from GenBank to conduct phylogenetic analyses. The individual segments of the BTV genome were analysed to determine if recent BTV-3 isolates are reassortants containing genomic segments from endemic US serotypes or if they retain a majority of Central American/Caribbean genotypes. The analyses indicate that BTV-3 isolates Mississippi 2006, Arkansas 2008 and Mississippi 2009 are closely related reassortants that contain five to six genomic segments that are of US origin and two to three segments of Central American/Caribbean origin. In contrast, the BTV-3 South Dakota 2012 isolate contains seven genomic segments that are more similar to isolates from Central American and the Caribbean. These different evolutionary histories of the BTV-3 isolates suggest that there are at least two different lineages of BTV-3 that are currently circulating in the US.

Teratogenic bluetongue and related orbivirus infections in pregnant ruminant livestock: timing and pathogen genetics are critical

Congenital infections of domestic animals with viruses in several families, including Bunyaviridae, Flaviridae, Parvoviridae, and Reoviridae, are the cause of naturally occurring teratogenic central nervous system and/or musculoskeletal defects (arthrogryposis) in domestic animals. Congenital infections of ruminant livestock with bluetongue virus (BTV) and some related members of the genus Orbivirus (family Reoviridae) have clearly shown the critical role of gestational age at infection in determining outcome. Specifically, fetuses infected prior to mid-gestation that survive congenital BTV infection are born with cavitating central nervous system defects that range from severe hydranencephaly to cerebral cysts (porencephaly). Generally, the younger the fetus (in terms of gestational age) at infection, the more severe the teratogenic lesion at birth. Age-dependent virus infection and destruction of neuronal and/or glial cell precursors that populate the developing central nervous system are responsible for these naturally occurring virus-induced congenital defects of animals, thus lesions are most severe when progenitor cells are infected prior to their normal migration during embryogenesis. Whereas congenital infection is characteristic of certain BTV strains, notably live-attenuated (modified-live) vaccine viruses that have been passaged in embryonating eggs, transplacental transmission is not characteristic of many field strains of the virus and much remains to be determined regarding the genetic determinants of transplacental transmission of individual virus strains.

Sequence analysis and evaluation of the NS3/A gene region of bluetongue virus isolates from South Africa

Phylogenetic networks and sequence analysis allow a more accurate understanding of the serotypes, genetic relationships and epidemiology of viruses. Based on gene sequences of the conserved segment 10 (NS3), bluetongue virus (BTV) can be divided into five topotypes. In this molecular epidemiology study, segment 10 sequence data of 11 isolates obtained from the Virology Section of the Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, were analyzed and compared to sequence data of worldwide BTV strains available in the GenBank database. The consensus nucleotide sequences of NS3/A showed intermediate levels of variation, with the nucleotide sequence identity ranging from 79.72 % to 100 %. All 11 strains demonstrated conserved amino acid characteristics. Phylogenetic networks were used to identify BTV topotypes. The phylogeny obtained from the nucleotide sequence data of the NS3/A-encoding gene presented three major and two minor topotypes. The clustering of strains from different geographical areas into the same group indicated spatial spread of the segment 10 genes, either through gene reassortment or through the introduction of new strains from other geographical areas via trade. The effect of reassortment and genetic drift on BTV and the importance of correct serotyping to identify viral strains are highlighted.

Reassortment between two serologically unrelated bluetongue virus strains is flexible and can involve any genome segment

Coinfection of a cell by two different strains of a segmented virus can give rise to a "reassortant" with phenotypic characteristics that might differ from those of the parental strains. Bluetongue virus (BTV) is a double-stranded RNA (dsRNA) segmented virus and the cause of bluetongue, a major infectious disease of livestock. BTV exists as at least 26 different serotypes (BTV-1 to BTV-26). Prompted by the isolation of a field reassortant between BTV-1 and BTV-8, we systematically characterized the process of BTV reassortment. Using a reverse genetics approach, our study clearly indicates that any BTV-1 or BTV-8 genome segment can be rescued in the heterologous "backbone." To assess phenotypic variation as a result of reassortment, we examined viral growth kinetics and plaque sizes in in vitro experiments and virulence in an experimental mouse model of bluetongue disease. The monoreassortants generated had phenotypes that were very similar to those of the parental wild-type strains both in vitro and in vivo. Using a forward genetics approach in cells coinfected with BTV-1 and BTV-8, we have shown that reassortants between BTV-1 and BTV-8 are generated very readily. After only four passages in cell culture, we could not detect wild-type BTV-1 or BTV-8 in any of 140 isolated viral plaques. In addition, most of the isolated reassortants contained heterologous VP2 and VP5 structural proteins, while only 17% had homologous VP2 and VP5 proteins. Our study has shown that reassortment in BTV is very flexible, and there is no fundamental barrier to the reassortment of any genome segment. Given the propensity of BTV to reassort, it is increasingly important to have an alternative classification system for orbiviruses.

Bluetongue virus genetic and phenotypic diversity: towards identifying the molecular determinants that influence virulence and transmission potential

Bluetongue virus (BTV) is the prototype member of the Orbivirus genus in the family Reoviridae and is the aetiological agent of the arthropod transmitted disease bluetongue (BT) that affects both ruminant and camelid species. The disease is of significant global importance due to its economic impact and effect on animal welfare. Bluetongue virus, a dsRNA virus, evolves through a process of quasispecies evolution that is driven by genetic drift and shift as well as intragenic recombination. Quasispecies evolution coupled with founder effect and evolutionary selective pressures has over time led to the establishment of genetically distinct strains of the virus in different epidemiological systems throughout the world. Bluetongue virus field strains may differ substantially from each other with regards to their phenotypic properties (i.e. virulence and/or transmission potential). The intrinsic molecular determinants that influence the phenotype of BTV have not clearly been characterized. It is currently unclear what contribution each of the viral genome segments have in determining the phenotypic properties of the virus and it is also unknown how genetic variability in the individual viral genes and their functional domains relate to differences in phenotype. In order to understand how genetic variation in particular viral genes could potentially influence the phenotypic properties of the virus; a closer understanding of the BTV virion, its encoded proteins and the evolutionary mechanisms that shape the diversity of the virus is required. This review provides a synopsis of these issues and highlights some of the studies that have been conducted on BTV and the closely related African horse sickness virus (AHSV) that have contributed to ongoing attempts to identify the molecular determinants that influence the virus' phenotype. Different strategies that can be used to generate BTV mutants in vitro and methods through which the causality between particular genetic modifications and changes in phenotype may be determined are also described. Finally examples are highlighted where a clear understanding of the molecular determinants that influence the phenotype of the virus may have contributed to risk assessment and mitigation strategies during recent outbreaks of BT in Europe.

Sequence analysis of the S10 gene of six Bluetongue Virus isolates from India

Bluetongue Virus (BTV) genome segment 10 (S10)-based phylogenetic studies are important in understanding the BTV evolution. S10 gene-based phylogenetic analysis grouped six different BTV isolates (BTV serotype 1, 18 and 23) from India in subclade A1 and showed closer relationship with BT viruses from Mediterranean Basin. Indian BTV serotypes 18 and 23 formed a single cluster distinct from BTV serotype 1 isolates and were evolved from BTV from China, Indonesia and Australia. The overall S10 sequences of BTV isolates from India were largely conserved (>95.7% homology) and were distinct from other BT viruses of the world.

A review of RT-PCR technologies used in veterinary virology and disease control: sensitive and specific diagnosis of five livestock diseases notifiable to the World Organisation for Animal Health

Real-time, reverse transcription polymerase chain reaction (rRT-PCR) has become one of the most widely used methods in the field of molecular diagnostics and research. The potential of this format to provide sensitive, specific and swift detection and quantification of viral RNAs has made it an indispensable tool for state-of-the-art diagnostics of important human and animal viral pathogens. Integration of these assays into automated liquid handling platforms for nucleic acid extraction increases the rate and standardisation of sample throughput and decreases the potential for cross-contamination. The reliability of these assays can be further enhanced by using internal controls to validate test results. Based on these advantageous characteristics, numerous robust rRT-PCRs systems have been developed and validated for important epizootic diseases of livestock. Here, we review the rRT-PCR assays that have been developed for the detection of five RNA viruses that cause diseases that are notifiable to the World Organisation for Animal Health (OIE), namely: foot-and-mouth disease, classical swine fever, bluetongue disease, avian influenza and Newcastle disease. The performance of these tests for viral diagnostics and disease control and prospects for improved strategies in the future are discussed.

Segment 10 based molecular epidemiology of bluetongue virus (BTV) isolates from Turkey: 1999-2001

Bluetongue is a significant arbovirus infection that has a negative impact on ruminant productivity in Turkey. Twenty-one Turkish BTV isolates were analyzed phylogenetically, based on genome segment 10 (Seg-10) nucleotide sequences. These analyses were used to explore the epidemiological background of individual isolates from both a regional and global perspective. In the regional analysis, the different BTV strains fell into two groups (Group 1 and Group 2). The Turkish virus isolates were localized in Group 1 which contains two sub-groups. The neighbor-joining analysis revealed that Seg-10 of majority of the Turkish viruses was closely related to certain other virus strains allocated in the eastern lineage. The Seg-10's of two viruses (TR25 and TR26) were more closely related to strains isolated in the Asia-Australia region. These strains belong to the 'eastern' topotype identified by [Maan, S., Maan, N.S., Ross-Smith, N., Batten, C.A., Shaw, A.E., Anthony, S.J., Samuel, A.R., Darpel, K.E., Veronesi, E., Oura, C.A.L., Singh,K.P., Nomikou, K., Potgieter, A.C., Attoui, H., van Rooij, E., van Rijn, P., De Clercq, K., Vandenbussche, F., Zientara, S., Bréard, E., Sailleau, C., Beer, M., Hoffman, B., Mellor, P.S., Mertens, P.P.C., 2008. Sequence analysis of bluetongue virus serotype 8 from the Netherlands 2006 and comparison to other European strains. Virology 377, 308-318]. Comparisons of amino acid sequences deduced from the Seg-10 genes showed a high level of conservation in the NS3/3A proteins from the Turkish viruses. The more frequent amino acid substitutions were identified by multiple alignment analysis, and one of the isolates (TR23) was remarkably found to be genetically quite distinct from the other isolates.

The NS3 proteins of global strains of bluetongue virus evolve into regional topotypes through negative (purifying) selection

Comparison of the deduced amino acid sequences of the genes (S10) encoding the NS3 protein of 137 strains of bluetongue virus (BTV) from Africa, the Americas, Asia, Australia and the Mediterranean Basin showed limited variation. Common to all NS3 sequences were potential glycosylation sites at amino acid residues 63 and 150 and a cysteine at residue 137, whereas a cysteine at residue 181 was not conserved. The PPXY and PS/TAP late-domain motifs were conserved in all but three of the viruses. Phylogenetic analyses of these same sequences yielded two principal clades that grouped the viruses irrespective of their serotype or year of isolation (1900-2003). All viruses from Asia and Australia were grouped in one clade, whereas those from the other regions were present in both clades. Each clade segregated into distinct subclades that included viruses from single or multiple regions, and the S10 genes of some field viruses were identical to those of live-attenuated BTV vaccines. There was no evidence of positive selection on the S10 gene as assessed by reconstruction of ancestral codon states on the phylogeny, rather the functional constraints of the NS3 protein are expressed through substantial negative (purifying) selection.

Phylogenetic comparison of the S10 genes of recent isolates of bluetongue virus from the United States and French Martinique Island

The sequences of the S10 genes of 28 recent isolates (1994-2004) of bluetongue virus (BTV) from the United States (US) and French Martinique Island (2006) in the Caribbean Basin were compared in phylogenetic analyses to those of viruses previously isolated in the same regions. Although the analyses segregated the recent virus isolates from the two regions into distinct topotype clusters, the analyses also confirm that viruses from the US and the Caribbean Basin/Central America can share similar S10 genes despite the fact that distinct constellations of BTV serotypes occur in the two regions.

Molecular epidemiology of bluetongue virus serotype 4 isolated in the Mediterranean Basin between 1979 and 2004

The nucleotide sequences of genome segments 2, 7, 8, 9 and 10, coding for viral proteins (VP) and non-structural proteins (NS)--VP2, VP7, NS2, VP6 and NS3/NS3A, respectively, were determined and compared for 10 strains of bluetongue virus (BTV) serotype 4 isolated in the Mediterranean Basin between 1979 and 2004, and the South African attenuated BTV 4 vaccine strain. The sequence data generated for the BTV 4 strains isolated in Greece in 1979, 1999 and 2000 showed that they had a common origin but were distinct from the lineage of the BTV 4 strains isolated from 2003 onward in the western Mediterranean Basin (Italy, Morocco, Spain and Corsica). The nucleotide and deduced amino acid (aa) sequences of the BTV 4 strains within each lineage were identical to each other, irrespective of the year of isolation or the geographical location. Although the sequence of VP2 from the Turkish and Greek strains were highly similar, there were sufficient differences in the VP6, VP7 and NS2 proteins to suggest that the Turkish BTV 4 belongs to a third lineage. Alignment of the NS3 sequences from the attenuated BTV 4 vaccine strain and the field strains showed 13 aa substitutions, which may, either singularly or together, be responsible for attenuation and hence determining the virulence of the virus.

Differentiation between field and vaccine strain of bluetongue virus serotype 16

In August 2000, bluetongue virus (BTV) appeared for the first time in Sardinia and, since then, the infection spread across Sicily and into the mainland of Italy involving at the beginning serotypes 2 and 9 and then, from 2002, 4 and 16. To reduce direct losses due to disease and indirect losses due to new serotype circulation, the 2004 Italian vaccination campaign included the modified-live vaccines against BTV-4 and 16 produced by Onderstepoort Biological Product (OBP), South Africa. Few months after the end of the campaign, BTV-16 was reported broadly in the country and the need of differentiating field from the BTV-16 vaccine isolate became crucial. In this study, the gene segments 2, 5, 6 and 10 of both the Italian and vaccine BTV-16 strains were sequenced and their molecular relationship determined. As sequences of segment 5 were those showing the highest differences (17.3%), it was possible to develop a new diagnostic tool able to distinguish the Italian BTV-16 NS1 gene from that of the homologous vaccine strain. The procedure based on the use of a RT-PCR and the subsequent sequencing of the amplified product showed a high degree of sensitivity and specificity when samples from either BTV-16 vaccinated or infected sheep were tested.

Rapid detection and quantitation of Bluetongue virus (BTV) using a Molecular Beacon fluorescent probe assay

Bluetongue virus (BTV) is the causative agent of Bluetongue (BT) disease in ruminant livestock and occurs almost worldwide between latitudes 35 degrees S and 50 degrees N; 24 serotypes of BTV are known of which 8 circulate periodically within parts of the Mediterranean Region. A fast (about 3.5 h) and versatile diagnostic procedure able to detect and quantify BTV-RNA, has been developed using a Molecular Beacon (MB) fluorescent probe; PCR primers were designed to target 91 bp within the NS3 conserved region of the viral RNA segment 10 (S10) and bracketed the MB fluorescence probe hybridisation site. The MB fluorescent probe was used to develop two Bluetongue serogroup-specific assays: a quantitative real time reverse transcriptase polymerase chain reaction (RT-PCR) and a traditional RT-PCR. These were tested using BTV-RNAs extracted from the blood and organs of BT-affected animals, and from virus isolate suspensions. The samples included ten serotypes (BTV-1-BTV-9 and BTV-16); of these, BTV serotypes -1, -2, -4, -9 and -16 have since 1998 been involved in the extensive outbreaks of BT across the Mediterranean Region. To evaluate the specificity and sensitivity of the MB probe, all positive samples (and negative controls) were tested using the developed quantitative real time RT-PCR and traditional RT-PCR assays. The former test had a detection limit of 10(3) cDNA molecules per reaction with a log-linear quantification range of up to 10(11) (R2 = 0.98), while the latter test was able to detect 500 cDNA-BTV molecules/PCR. The results show that the MB fluorescent probe is both rapid and versatile for the laboratory diagnosis of Bluetongue and for quantifying levels of viraemia in BTV-affected animals. An "in silico" comparison of the primers and MB fluorescent probe used in this study showed that it is possible to detect all 24 serotypes of BTV.

VP2-segment sequence analysis of some isolates of bluetongue virus recovered in the Mediterranean basin during the 1998-2003 outbreak

The complete nucleotide sequences of the VP2 segments of bluetongue virus (BTV) isolates recovered from Italy, Greece and Israel, from 1998 to 2003, were determined. Phylogenetic analysis of these sequences, those from related viruses and the South African vaccine strains, were used to determine the probable geographic origin of BTV incursions into Italy. Results indicated that viruses from each of the four serotypes isolated in Italy (2, 4, 9 and 16) possibly had a different origin. Analysis of the bluetongue virus serotype 2 (BTV-2) isolates gave evidence that this serotype probably moved from Tunisia. BTV-4 results showed probable incursion from the southwest and not from Greece or Israel. BTV-9 isolates clearly have an eastern origin (most probably Greece), whereas BTV-16 isolates are indistinguishable from the BTV-16 live attenuated vaccine strain. The phylogenetic findings were supported by polyacrylamide gel electrophoresis (PAGE) analysis of the complete amplified genome of each isolate except for BTV-16 Italian field isolate, which showed a slightly different PAGE profile. A combination of the complete VP2 sequencing and PAGE analysis of complete genomes, allowed not only phylogenetic analysis, but also vaccine detection and assessment of reassortment events.

Molecular epidemiology of Bluetongue virus in northern Colorado

The molecular epidemiology of Bluetongue virus serotype 11 (BTV11) in an enzootic focus in northern Colorado was investigated. Viruses isolated up to 12 years apart, from both vertebrate and invertebrate hosts, were compared by phylogenetic analysis of nucleotide sequence data from three genome segments: L2, S7, and S10. For each segment, viruses isolated from ruminants in the 1980s were more similar to one another than to viruses isolated from Culicoides spp. insects in the 1990s. Nearly identical BTV11-L2 segments were found in all isolates, but over time they were associated with different S7 and S10 genome segments. Therefore, L2-segment-based serologic identification of BTV isolates underestimates the origin and natural evolution of the viruses. In addition, the use of one or even two genome segments is inadequate to define the molecular epidemiology of the viruses in an enzootic focus. This information could influence import/export regulations based on BTV epidemiology in enzootic areas, as well as our view of the natural biology of the viruses.

Molecular analysis of the NS3/NS3A gene of Bluetongue virus isolates from the 1979 and 1998–2001 epizootics in Greece and their segregation into two distinct groups

The sequence of the genome segment 10 (Seg-10) encoding NS3/NS3A was determined for 19 field isolates of Bluetongue virus (BTV) of serotypes BTV-1, BTV-4, BTV-9 and BTV-16, derived from epizootics in Greece in the years 1979 and 1998-2001. The aim of the study was to define the molecular epidemiology of the virus in this part of the Mediterranean basin. On the basis of the Seg-10 sequences, the isolates grouped into two distinct phylogenetic clusters. These were Greek group I of solely serotype BTV-4 viruses, and Greek group II of serotypes BTV-1, BTV-9 and BTV-16 viruses. The isolates in Greek group I clustered with the Corsican and Tunisian BTV-2 serotypes and US group II strains of BTV-10 and BTV-13 serotypes, while those in Greek group II with Chinese, Indian and Australian viruses of different serotypes suggesting that viruses derived from two distinct ecosystems have caused BT incursions in Greece over the last 25 years. The NS3/NS3A sequences of most of the BTV-4 isolates were identical, irrespective of the year of isolation, geographical location and host species or tissue origin. Maximum of 15-16% nucleic acid sequence variation, but only 4% deduced amino acid substitution, were observed between groups I and II. Furthermore, the clustering of the NS3/NS3A sequences was independent of the viral serotype, indicating the occurrence of genome segment reassortment during the course of evolution of the viruses.

Genetic variation among epizootic hemorrhagic disease viruses in the southeastern United States: 1978–2001

The epizootic hemorrhagic disease (EHD) viruses, which are endemic in the southeastern United States, are the causative agents of an important clinical disease in wild and captive ruminants. In order to elucidate the molecular epidemiology of EHD serotype 2, the sequences of portions of the S10 and L2 gene segments (which encode the NS3 viral egress protein and the VP2 surface protein, respectively) of viral isolates made from white-tailed deer over 23 years(1978-2001) were determined and compared using phylogenetic analyses. Both loci demonstrated very little genetic variation among isolates, with a 94-100% nucleotide identity among isolates at the S10 locus (98-100% amino acid conservation), and an 89.1-100% identity among isolates at the L2 locus (87.6-100% amino acid conservation). The grouping of isolates within the resulting cladograms appeared nearly random with respect to time of isolation and geographic origin. One exception to this was a distinctive grouping of some isolates from 1996 to 1997, which formed a separate subclade in both the S10 and L2 cladograms.

Differentiation of Italian field and South African vaccine strains of bluetongue virus serotype 2 using real-time PCR

The current outbreaks of bluetongue (BT) disease in sheep in the central parts of the Mediterranean basin are being combated by extensive vaccination to control further spread of the virus and to suppress its long-term maintenance in the field. To be able to monitor the success of this campaign, and to be able to identify new foci of the disease, it is necessary to harness diagnostic methods, both rapid and sensitive, for differentiating reliably field from vaccine strains of bluetongue virus (BTV). A new method is described for their differentiation using fluorescence resonance energy transfer (FRET) probes with real-time PCR. The method is based on the principle that the melting temperature of a DNA duplex gives information about the sequence, and allows even double-base alterations in the amplicon to be identified. The RT-PCR, the generation of melting curves, and fluorescence detection were all performed using the LightCycler system (Roche Diagnostics, Mannheim, Germany).

Evidence of segment reassortment in Crimean-Congo haemorrhagic fever virus

The complete nucleotide sequences of the small (S) and medium (M) segments of three independent strains of Crimean-Congo haemorrhagic fever (CCHF) virus isolated in Uzbekistan, Iraq and Pakistan have been determined. Partial S and M segment sequences from two additional strains and partial large segment sequences from five strains of CCHF virus have also been obtained. These data have been compiled and compared with published full-length and partial sequences of other CCHF virus strains. Analysis of virus strains for which complete and partial S and M segment sequences are available reveals that the phylogenetic grouping of some strains differ between these two segments. Data provided in this report suggest that this discrepancy is not the result of recombination, but rather the consequence of reassortment events that have occurred in some virus lineages. Although described in other genera of the Bunyaviridae family, this is the first report of segment reassortment occurring in the Nairovirus genus.

Genetic diversity of bluetongue viruses in south east Asia

Bluetongue viruses (BTV) were isolated from sentinel cattle in Malaysia and at two sites in Indonesia. We identified eight serotypes some of which appeared to have a wide distribution throughout this region, while others were only isolated in Malaysia or Australia. Nearly half of the 24 known BTV serotypes have now been identified in Asia. Further, we investigated the genetic diversity of their RNA segments 3 and 10. Using partial nucleotide sequences of the RNA segment 3 (540 bp) which codes for the conserved core protein (VP3), the BTV isolates were found to be unique to the previously defined Australasian topotype and could be further subdivided into four distinct clades or genotypes. Certain of these genotypes appeared to be geographically restricted while others were distributed widely throughout the region. Similarly, the complete nucleotide sequences of the RNA segment 10 (822 bp), coding for the non-structural protein (NS3/3A), were also conserved and grouped into the five genotypes; the BTV isolates could be grouped into three Asian genotypes and two Nth American/Sth African genotypes.

VP2 gene phylogenetic characterization of field isolates of African horsesickness virus serotype 7 circulating in South Africa during the time of the 1999 African horsesickness outbreak in the Western Cape

We present the first VP2-gene phylogenetic analysis of African horsesickness (AHS) viruses within a serotype. Thirteen AHSV 7 isolates were obtained from cases that occurred in South Africa during 1998-1999, and three were historical AHSV 7 isolates. The goals were to start a database of isolates of known location and time of isolation and to determine if we could identify the origin of an AHS outbreak in the surveillance area in the Western Cape. We prepared full-length cDNA copies of the VP2-genes of the isolates. Nucleic acid sequence data of a 786 bp region was used to characterize the genetic relationships between the isolates. The nucleic acid identities between the isolates ranged from 95.5 to 100%. Isolates from common geographical regions grouped together. Characterization of field isolates revealed the presence of two AHSV 7 lineages in South Africa during this period. The grouping of the viruses into two clades accurately reflected the geographical groupings of the isolates. The average nucleic acid divergence between the clades was 4.3%. Within the clades the divergence was 0.5 and 0.1%, respectively. The data suggests that the AHS outbreak in the Western Cape could have been an incursion from the Kwazulu Natal Province.

Variation in the NS3 gene and protein in South African isolates of bluetongue and equine encephalosis viruses

Bluetongue virus (BTV) and equine encephalosis virus (EEV) are agriculturally important orbiviruses transmitted by biting midges of the genus Culicoides. The smallest viral genome segment, S10, encodes two small nonstructural proteins, NS3 and NS3A, which mediate the release of virus particles from infected cells and may subsequently influence the natural dispersion of these viruses. The NS3 gene and protein sequences of South African isolates of these viruses were determined, analysed and compared with cognate orbivirus genes from around the world. The South African BTV NS3 genes were found to have the highest level of sequence variation for BTV (20 %), while the highest level of protein variation of BTV NS3 (10 %) was found between South African and Asian BTV isolates. The inferred NS3 gene phylogeny of the South African BTV isolates grouped them with BTV isolates from the United States, while the Asian BTV isolates grouped into a separate lineage. The level of variation found in the NS3 gene and protein of EEV was higher than that found for BTV and reached 25 and 17 % on the nucleotide and amino acid levels, respectively. The EEV isolates formed a lineage independent from that of the other orbiviruses. This lineage segregated further into two clusters that corresponded to the northern and southern regions of South Africa. The geographical distribution of these isolates may be related to the distribution of the Culicoides subspecies that transmit them.

Variation in the NS3/NS3A gene of bluetongue viruses contained in Culicoides sonorensis collected from a single site in southern California

To determine the variability of the NS3/NS3A gene of field strains of BTV contained in Culicoides sonorensis collected from a single site in California (CA), the NS3/NS3A gene was directly amplified and sequenced from 22 pools of C. sonorensis and compared with those of previously characterized field isolates from CA, as well as to viruses that caused recent outbreaks of bluetongue disease in ruminants in CA. Phylogenetic analysis established that the NS3/NS3A gene of strains of BTV contained in C. sonorensis collected from the site exists as a heterogeneous population. The two most divergent nucleotide sequences of the NS3/NS3A genes of these viruses differed by 2.5% (18 nucleotides). Comparison with the NS3/NS3A gene sequences from viruses that caused recent instances of bluetongue disease in ruminants in CA indicated that BTV strains from different geographic regions can exhibit a higher degree of genetic heterogeneity (up to 6.6%; 0-48 nucleotide differences) than those contained in C. sonorensis collected from a single site.

Bluetongue virus diagnosis of clinical cases by a duplex reverse transcription-PCR: a comparison with conventional methods

A duplex reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of bluetongue virus (BTV) in clinical samples was developed. This assay, which detects the highly conserved S10 region of BTV, was assessed for sensitivity and application as a rapid and dependable diagnostic tool by comparison with standard assays of virus detection, such as virus isolation in embryonated chicken eggs and cell culture. Simultaneous detection of BTV and host beta-actin RNAs minimizes the possibility of false negative results. The sensitivity of the assay was found to be equal to five cell culture infectious dose (CCID(50)) units and its specificity was confirmed as no RT-PCR product was detected with RNAs from two closely related orbiviruses, i.e. epizootic haemorrhagic disease virus (serotypes 1, 2 and 318) and African horse sickness virus, serotype 9, or RNAs from uninfected BHK-21 cells and blood samples from uninfected sheep or goats. In this study, 36 blood samples from naturally infected mixed flocks of sheep and goats were examined. Seventeen animals were identified as BTV-positive by RT-PCR, whereas only 13 were found positive by virus isolation in embryonated chicken eggs and nine by cell culture assays. These results indicate that the duplex RT-PCR could be a useful technique for monitoring BTV infection in the field.

Occurrence of genetic drift and founder effect during quasispecies evolution of the VP2 and NS3/NS3A genes of bluetongue virus upon passage between sheep, cattle, and Culicoides sonorensis

Bluetongue virus (BTV) is the cause of an insect-transmitted virus infection of ruminants that occurs throughout much of the world. Individual gene segments differ between field strains of BTV; thus, we hypothesized that key viral genes undergo genetic drift during alternating passage of BTV in its ruminant and insect hosts. To test this hypothesis, variation in the consensus sequence and quasispecies heterogeneity of the VP2 and NS3/NS3A genes of a plaque-purified strain of BTV serotype 10 was determined during alternating infection of vector Culicoides sonorensis and a sheep and calf. Consensus sequences were determined after reverse transcriptase-nested PCR amplification of viral RNA directly from ruminant blood and homogenized insects, and quasispecies heterogeneity was determined by the sequencing of clones derived from directly amplified viral RNA. Comparison of these sequences to those of the original BTV inoculum used to initiate the cycle of BTV infection demonstrated, for the first time, that individual BTV gene segments evolve independently of one another by genetic drift in a host-specific fashion, generating quasispecies populations in both ruminant and insect hosts. Furthermore, a unique viral variant was randomly ingested by C. sonorensis insects that fed on a sheep with low-titer viremia, thereby fixing a novel genotype by founder effect. Thus, we conclude that genetic drift and founder effect contribute to diversification of individual gene segments of field strains of BTV.

Membrane association of African horsesickness virus nonstructural protein NS3 determines its cytotoxicity

The smallest RNA genome segment of African horsesickness virus (AHSV) encodes the nonstructural protein NS3 (24K). NS3 localizes in areas of plasma membrane disruption and is associated with events of viral release. Conserved features in all AHSV NS3 proteins include the synthesis of a truncated NS3A protein from the same open reading frame as that of NS3, a proline-rich region, a region of strict sequence conservation and two hydrophobic domains. To investigate whether these features are associated with the cytotoxicity of NS3 or altered membrane permeability, a series of mutants were constructed and expressed in the BAC-TO-BAC baculovirus-expression system. Our results indicate that mutations in either of the two hydrophobic domains do not prevent membrane targeting of the mutant proteins but abolish their membrane anchoring. This prevents their localization to the cell surface and obviates their cytotoxic effect. The cytotoxicity of NS3 is therefore dependent on its membrane topography and thus involves both hydrophobic domains. NS3 has many of the characteristics of lytic viral proteins that play a central role in viral pathogenesis through modifying membrane permeability.

Variation of African horsesickness virus nonstructural protein NS3 in southern Africa

NS3 protein sequences of recent African horsesickness virus (AHSV) field isolates, reference strains and current vaccine strains in southern Africa were determined and compared. The variation of AHSV NS3 was found to be as much as 36.3% across serotypes and 27.6% within serotypes. NS3 proteins of vaccine and field isolates of a specific serotype were found to differ between 2.3% and 9.7%. NS3 of field isolates within a serotype differed up to 11.1%. Our data indicate that AHSV NS3 is the second most variable AHSV protein, the most variable being the major outer capsid protein, VP2. The inferred phylogeny of AHSV NS3 corresponded well with the described NS3 phylogenetic clusters. The only exception was AHSV-8 NS3, which clustered into different groups than previously described. No obvious sequence markers could be correlated with virulence. Our results suggest that NS3 sequence variation data could be used to distinguish between field isolates and live attenuated vaccine strains of the same serotype.

Identification of seven serotypes of bluetongue virus from the People's Republic of China

Seven serotypes (1, 2, 3, 4, 12, 15 and 16) of bluetongue virus were isolated from the blood of sheep and cattle in the People's Republic of China between 1986 and 1996. Six of these viruses were isolated in Yunnan province. The sheep from which serotypes 1 and 16 were isolated showed obvious signs of bluetongue disease, whereas the cattle from which serotypes 2, 3, 4, 12 and 15 were isolated were clinically normal. Phylogenetic analyses of these viruses indicate that they are more closely related to one another, and to an Australian strain of serotype 1, than they are to prototype strains of bluetongue virus serotypes 2, 10, 11, 13 and 17 from the USA.

Sequence comparison of the L2 and S10 genes of bluetongue viruses from the United States and the People's Republic of China

Bluetongue virus (BTV) infection of ruminants is endemic throughout much of the US and China. The S10 and a portion of the L2 gene segments of Chinese prototype strains of BTV serotypes 1, 2, 3, 4, 12, 15, and 16 were sequenced and compared to the same genes of prototype and field strains of BTV from the US. Phylogenetic analysis of the S10 gene segregated the Chinese viruses into a monophyletic group distinct from the US viruses, whereas similar analysis of the L2 gene segregated strains of BTV according to serotype, regardless of geographic origin.