Genetic diversity of the S10 RNA segment of field and vaccine strains of bluetongue virus from the P. R. China

Bluetongue virus (BTV) infection of ruminants is endemic throughout tropical and subtropical regions of the world. However, the molecular epidemiology of BTV infection in China has not yet been reported. In this study, the S10 gene segments from 30 BTV isolates, one attenuated BTV strain, one vaccine BTV strain, and one South Africa BTV prototype strain, were sequenced. Phylogenetic analysis of the S10 genes showed that Chinese BTV isolates could be classified into two phyletic subgroups, and the clustering of Chinese BTV viruses was dependent on their geographical origin and the number of generations for which they had been propagated, rather than their host species or year of isolation.     

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.     

Phylogenetic analysis of the S7 gene does not segregate Chinese strains of bluetongue virus into a single topotype

Summary.  Bluetongue virus (BTV) infection of ruminants is endemic throughout tropical and subtropical regions of the world. The S7 gene segments of prototype Chinese strains of BTV serotypes 1, 2, 3, 4, 12, 15, and 16 were sequenced and compared to the same genes of prototype strains of BTV from the US, Australia, and South Africa. The S7 genes and predicted VP7 proteins of the Chinese viruses were relatively conserved, with the notable exception of serotype 15. Furthermore, phylogenetic analysis of the S7 genes did not predict geographic origin of the various strains of BTV. Received August 28, 1999 Accepted December 7, 1999     

A duplex RT-PCR assay for detection of genome segment 7 (VP7 gene) from 24 BTV serotypes

Since 1998, six distinct serotypes of Bluetongue virus (BTV) have invaded Southern and Central Europe, persisting in some regions for up to 6 years and resulting in the deaths of >1.8 million sheep. Rapid and reliable methods of virus detection and identification play an essential part in our fight against bluetongue disease (BT). We have therefore developed and evaluated a duplex, one-step RT-PCR assay that detects genome segment 7 (encoding the major serogroup (virus-species) specific antigen and outer-core-protein VP7) from any of the 24 BTV serotypes. Although Seg-7 is highly conserved, there are sequence differences in the near terminal regions that identify two distinct phylogenetic groups. Two sets of primers (targeting Seg-7 terminal regions of viruses from these two groups) were included in a duplex RT-PCR assay system. Assay sensitivity was evaluated using tissue culture derived virus, infected vector insects and clinical samples (blood and other tissues). The assay reliably amplified Seg-7 from any of the BTV strains tested, including isolates of the 24 BTV serotypes and isolates from different geographic origins. No cross-reactions were detected with members of closely related Orbivirus species (African horsesickness virus (AHSV), Epizootic haemorrhagic disease virus (EHDV), Equine encephalosis virus (EEV) and Palyam virus (PALV)).     

Bluetongue virus evolution: sequence analyses of the genomic S1 segments and major core protein VP7.

The S1 segments, encoding the group-specific antigen, VP7, from the five United States prototype BTV serotypes were cloned as full-length entities. The nucleotide and deduced amino acid sequences of segment S1 of BTV-2 were determined and compared with BTV-10, -11, -13, and -17, completing the sequencing of this cognate gene segment from all five US BTV serotypes. Each segment is 1156 bp long and contains an open reading frame encoding the 349-amino acid VP7 protein. Most (greater than 94%) of the amino acids of VP7 among the serotypes are conserved, including the location (position 255) of a single lysine residue. Secondary structure analyses of VP7 predict a putative eight-stranded beta-barrel between amino acid positions 150 and 250, a structure similar to that observed in ssRNA viruses. The S1 genes are flanked by conserved 5' and 3' noncoding regions. Stem-loop structures are predicted at the 3' end of each gene (nucleotide positions 1058-1097). The S1 segments of BTV-2, -10, -11, and -17 have greater than 93% of the nucleotides conserved, while less than 80% of their bases are identical with BTV-13. Analyses of nucleotide mismatches in each codon position of the VP7 open reading frame, transition frequencies, and evolutionary distances show that of the five, BTV-13 is the most distantly related and that BTV-10 and -17 are the most closely related serotypes. Evolutionary distance calculations of segment L2 from BTV-10, -11, and -17 concur with these observations. Comparison of this relationship with hybridization data of segment M3, which codes for VP5, suggests that BTV-17 has evolved by a combination of genetic drift and genomic reassortment. The data also indicate that the five US BTV serotypes are derived from two distinct gene pools. Evolution distances were used to estimate an evolution rate of 2.2 x 10(-3) nucleotide substitution/site/year for BTV segment S1. This rate is similar to the genes of retroviruses and implies an absence of RNA polymerase proofreading activity for dsRNA viruses.     

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.     

The genetic relatedness of a number of individual cognate genes of viruses in the bluetongue and closely related serogroups

Genome segments 2, 4, 6, 7, 8, 9, and 10 of bluetongue virus (BTV) serotype 10 were cloned in pBR322. The 2926-bp S2 gene, which codes for the serotype-specific antigen, was cloned as two overlapping 2.4-kb inserts. The relatedness of cognate S2 genes among different isolates of BTV10 was investigated by hybridization, restriction enzyme mapping, and sequencing of the terminal ends. Hybridization under high stringency conditions indicated a genetic diversity between isolates of BTV10 from South Africa and the United States. This was confirmed by a comparison of the restriction map of the cloned S2 gene of a BTV10 isolate from South Africa to that of the S2 gene of the BTV10 strain of the United States which has been cloned and sequenced by Purdy et al. (1985). The part of the genome that was sequenced indicated, however, that this variation was confined to an approximately 10% sequence divergence in the coding region. Very few of the nucleotide substitutions resulted in an amino acid change. The genetic variation of cognate BTV genes within the BTV serogroup as well as among different members of closely related serogroups was also investigated. DNA probes from cloned BTV10 segments were hybridized to dsRNA from 24 different BTV serotypes. Genome segments S2 and S6 were found to be almost equally serotype specific. The stringency of the wash solutions after hybridization can be manipulated to determine an order of relatedness of different cognate genes. This was illustrated by the hybridization of a sensitive RNA probe of S7 to different BTV serotypes as well as to dsRNA from closely related orbiviruses. The results confirmed a relatedness between BTV and members of the epizootic hemorrhagic disease virus (EHDV) serogroups.     

Genetic characterization of bluetongue virus serotype 9 isolates from India

Recent incursions of bluetongue virus (BTV) into previously naive geographical areas have emphasised the need to better understand virus movement and epidemiology. Several bluetongue virus (BTV) serotypes are known to exist in India, and some serotype viruses have been isolated. However, the complete genome of not a single isolate is available to date. We report the complete genome sequence of one, and partial sequences of three other Indian isolates of BTV-9. Evolutionary relationships with segment-2 and -6 sequences of BTV isolates around the world, deduced using four different phylogenetic analyses and a similarity programme, show that BTV-9 (Eastern), BTV-9 (Western), and BTV-5 form a triad of equidistant, genetically distinct groups of viruses. The Indian BTV-9 isolates were closely related to Mediterranean and European BTV-9 isolates (Eastern topotype) based on segment-2 and -6 sequences. By contrast, segment-5 analyses clustered the Indian BTV-9 isolates with South African BTV-3 reference strain (98% identity), which belongs to one of the Western types. These results have implications on BTV origin and movement, genotyping, serotyping, and vaccine design.     

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.     

Phylogenetic relationships of bluetongue viruses based on gene S7

Previous phylogenetic analyses based on bluetongue virus (BTV) gene segment L3, which encodes the inner core protein, VP3, indicated a geographical distribution of different genotypes. The inner core protein, VP7, of BTV has been identified as a viral attachment protein for insect cell infection. Because the inner core proteins are involved with infectivity of insect cells, we hypothesized that certain VP7 protein sequences are preferred by the insect vector species present in specific geographic locations. We compared the gene segment S7, which encodes VP7, from 39 strains of BTV isolated from Central America, the Caribbean Basin, the United States, South Africa and Australia. For comparison, the S7 sequences from strains of the related orbiviruses, epizootic hemorrhagic disease virus (EHDV) and African horse sickness virus (AHSV) were included. The S7 gene was highly conserved among BTV strains and fairly conserved among the other orbiviruses examined. VP7 sequence alignment suggests that the BTV receptor-binding site in the insect is also conserved. Phylogenetic analyses revealed that the BTV S7 nucleotide sequences do not unequivocally display geographic distribution. The BTV strains can be separated into five clades based on the deduced VP7 amino acid sequence alignment and phylogeny but evidence for preferential selection by available gnat species for a particular VP7 clade is inconclusive. Differences between clades indicate allowable variation of the VP7 binding protein.     

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.     

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.     

Molecular epidemiology of rabies in Ukraine

To investigate the circulation of rabies virus in Ukraine, 78 rabies virus isolates were acquired from 14 states in 2002 and 2008-2010 for characterization. Partial sequences of nucleoprotein (359 nt) and glycoprotein (344 nt) genes were compared with those from neighbouring countries. The analysis identified 39 unique nucleoprotein genes and two geographically distinct RV variants belonging to the cosmopolitan lineage. The Ukrainian samples were similar to the North-East European lineage (NEE) (n?=?19) and Russian group C (n?=?20). The group C viruses were mainly isolated in Eastern Ukraine, from 9 regions, and from two other regions in Western Ukraine, suggesting the presence of group C throughout the country. These group C viruses are intermixed in bordering regions along the Dnieper River with viruses of group NEE, which were mainly isolated in six regions in Western Ukraine. Both nucleoprotein and glycoprotein gene analyses suggested evidence for cross-border movements of rabies virus.     

Genetic variation among dengue 2 viruses of different geographic origin

Genetic variation in dengue 2 isolates from various geographic areas was examined by oligonucleotide fingerprinting of the 40 S genome RNA. Oligonucleotide maps of geographically isolated and epidemiologically unrelated viruses were very distinct. Direct comparison of the oligonucleotide map of the dengue 2 prototype New Guinea 2 virus, isolated in 1944, with the fingerprints of more recent isolates from the South Pacific indicated that the genome of dengue 2 virus had undergone extensive change although the viruses are serologically indistinguishable. The oligonucleotide map of an isolate from a recent case in Jamaica and a mosquito isolate from Upper Volta, Africa, were recognized to be almost identical, suggesting that virus may have been introduced into the Caribbean from West Africa. Likewise, the fingerprints of isolates from Puerto Rico and the South Pacific shared 80 to 95% of their large oligonucleotides, suggesting that the virus involved in these epidemics may have spread throughout Tahiti, American Samoa, Fiji, and to Puerto Rico in the Caribbean or vice versa. On the basis of these studies, five genetic variants or topotypes of dengue 2 virus have been established: (1) Puerto Rico-South Pacific, (2) Burma-Thailand, (3) the Seychelles, (4) the Philippines, and (5) Jamaica-West Africa. Oligonucleotide fingerprinting offers a highly sensitive and reproducible technical approach to the investigation of dengue 2 virus intratypic variation and possibly to the understanding of the biological variation associated with dengue fever and hemorrhagic disease.     

Analysis of genome segments from six different isolates of bluetongue virus using RNA-RNA hybridisation: a generalised coding assignment for bluetongue viruses

Nucleic acid probes prepared directly from bluetongue virus (BTV) genomic double-stranded RNA (dsRNA) have been used to identify the functionally equivalent genome segments from six distinct isolates of BTV after their separation in both agarose and polyacrylamide gel electrophoresis systems. Variations in the rate, and in one case the order, of migration of the equivalent genome segments from different viruses was detected in the polyacrylamide gel system. However, the genomic dsRNA profiles of eleven BTV isolates were found to be identical when analysed by agarose gel electrophoresis. Functionally equivalent genome segments from the six viruses that were analysed were found to migrate in identical relative positions in this gel system. From these data we propose a modified version of the protein coding assignments published for BTV 1 South Africa (Mertens et al., 1984) in which the identification of the genome segments would be based upon their order of migration in the agarose rather than the polyacrylamide gel system. The modified coding assignments, unlike the original assignments, would be applicable to all of those viruses analysed and appear likely to be valid for all normal BTV isolates.     

The complete nucleotide sequence of bluetongue virus serotype 1 RNA3 and a comparison with other geographic serotypes from Australia, South Africa and the United States of America, and with other orbivirus isolates

The sequence of the RNA segment 3 of bluetongue virus (BTV) serotype 1 from Australia is presented along with its deduced amino acid sequence. DNA copies of this genome segment were inserted either into the E. coli plasmid pBR322 by homopolymeric tailing or by direct insertion of double-stranded DNA fragments generated by restriction endonuclease cleavage into the appropriate M13 bacteriophage vectors (Vieira, J. and Messing, J., 1982, Gene 19, 259-268). Direct comparisons were made to the nucleotide sequence data of Purdy, M. et al., 1984 (J. Virol. 51, 754-759) and Ghiasi, H. et al., 1985 (Virus Res. 3, 181-190) for the United States of America (US) isolates of BTV, serotypes 10 and 17, respectively. A method for the rapid cloning, sequencing and alignment of orbivirus RNA 3 segments was utilised to compare other geographical isolates of BTV, as well as those of other orbivirus serotypes, in particular, epizootic haemorrhagic disease of deer virus (EHDV) and Warrego. The comparison of this sequence data reveals that BTV isolates can be separated into distinct geographical types which in turn are distinct from the other orbivirus isolates studied. The sequence conservation at the amino acid level for the gene product of RNA3 (VP3) does not enable distinctions to be made amongst the BTV isolates at a geographical level, but does afford easy distinction into the different orbivirus groups. A possible evolutionary schematic is presented for the orbiviruses studied.     

Nucleotide sequence of the genome segment encoding nonstructural protein NS1 of bluetongue virus serotype 20 from Australia

The nucleotide sequence of the genome segment (S6) encoding the nonstructural protein NS1 of an Australian isolate of bluetongue virus serotype 20 (BTV 20) has been determined from a series of overlapping cDNA clones synthesized using two terminal 15-mer oligonucleotides as primers. The gene consists of 1769 nucleotides with an open reading frame between nucleotides 35 and 1690 encoding a protein of 552 amino acids (molecular weight 64,506 Da; net charge –2 at pH 7). Comparison of the nucleotide and deduced amino acid sequence of this genome segment with cognate segments of isolates of BTV 1 from Australia and South Africa, and BTV 10 and BTV 17 from the United States, revealed homologies of 98%, 80%, 79%, and 79%, respectively, at the nucleotide level and 98%, 90%, 89%, and 90% identity, respectively, at the amino acid level. The data indicate that the evolutionary divergence between NS1 genes of two different Australian BTV serotypes (BTV 20 and BTV 1) is less than that between isolates of the same (BTV 1) or different serotypes from different geographical locations.The EMBL Data Library sequence accession Code is X56735 BLUETONGUE VIRUS RNA SEGMENT 6.     

Genetic relationships of bluetongue virus serotypes isolated from different parts of the world

Full-length DNA clones representing the 10 double-stranded RNA segments of US bluetongue virus serotype 10 (BTV-10) have been used in a study to determine the genetic relationships among 20 different BTV serotypes. The study was undertaken using Northern blot hybridization techniques involving 32P-labelled DNA probes and total RNA species extracted from BHK-21 cells infected with 20 different BTV serotypes. The results obtained indicate that all the genes representing the nonstructural proteins of BTV (NS1, NS2 and NS3) as well as most of the inner capsid polypeptides are highly conserved (e.g., VP1, VP3, VP4), while VP6 and VP7, the remaining two inner capsid components, are less conserved. The genes representing the two outer capsid polypeptides, VP2 and VP5, vary significantly. When complete DNA clones of RNA segment 2 (representing the VP2 neutralization gene) of 4 other US serotypes (BTV-2, -11, -13 and -17) and one Australian serotype (BTV-1) were used in similar hybridization studies, the data obtained showed that despite geographical distances, a certain BTV serotype exhibits similarities. Some hybridization signals were detected with several of the inner capsid genes and the corresponding RNA segments of epizootic hemorrhagic disease virus (EHDV), a distantly related orbivirus, although none of the BTV outer capsid genes, nor any of the nonstructural genes hybridized with either EHDV-1 or EHDV-2 RNA species.     

A simple restriction fragment length polymorphism-based strategy that can distinguish the internal genes of human H1N1, H3N2, and H5N1 influenza A viruses

A simple molecular technique for rapid genotyping was developed to monitor the internal gene composition of currently circulating influenza A viruses. Sequence information from recent H1N1, H3N2, and H5N1 human virus isolates was used to identify conserved regions within each internal gene, and gene-specific PCR primers capable of amplifying all three virus subtypes were designed. Subtyping was based on subtype-specific restriction fragment length polymorphism (RFLP) patterns within the amplified regions. The strategy was tested in a blinded fashion using 10 control viruses of each subtype (total, 30) and was found to be very effective. Once standardized, the genotyping method was used to identify the origin of the internal genes of 51 influenza A viruses isolated from humans in Hong Kong during and immediately following the 1997-1998 H5N1 outbreak. No avian-human or H1-H3 reassortants were detected. Less than 2% (6 of 486) of the RFLP analyses were inconclusive; all were due to point mutations within a restriction site. The technique was also used to characterize the internal genes of two avian H9N2 viruses isolated from children in Hong Kong during 1999.