Molecular and antigenic characterization of rabbit hemorrhagic disease virus isolated in Cuba indicates a distinct antigenic subtype

Summary. Phylogenetic analyses conducted on isolates of rabbit hemorrhagic disease virus (RHDV) from throughout the world have shown well-defined genogroups comprising representative strains of the virus and antigenic variants. In this work, we have isolated and characterized RHDV from the major epizootic that occurred in Cuba in 2004–2005. Sequence analysis of the capsid protein gene and antigenic characterization of this strain has allowed its inclusion as a member of the distinct RHDVa subtype. We also found that specific antibodies directed against RHDV reference strains bound to the Cuban isolate in a competition ELISA and inhibited virus hemagglutination in vitro. This is the second report on the molecular characterization of RHDVa circulating in the American region. First three authors contributed equally to this work.     

Phylogenetic analysis of rabbit haemorrhagic disease virus in France between 1993 and 2000, and the characterisation of RHDV antigenic variants

Summary.  The first molecular epidemiological study of Rabbit haemorrhagic disease virus undertaken in France between 1988 and 1995, identified three genogroups, two of which (G1, G2) disappeared quickly. We used immunocapture-RT-PCR and sequencing to analyse 104 new RHDV isolates collected between 1993 and 2000. One isolate was obtained in 2000 from a French overseas territory, the Reunion Island. The nucleotide sequences of these isolates were aligned with those of some French RHDV isolates representative of the three genogroups previously identified, of some reference strains and German and American RHDV antigenic variants. Despite the low degree of nucleotide sequence variation, three new genogroups (G4 to G6) were identified with significant bootstrap values. Two of these genogroups (G4 and G5) were related to the year in which the RHDV isolates were collected. Genogroup G4 emerged from genogroup G3, which has now disappeared. Genogroup G5 is a new independent group. The genogroup G6 contained an isolate collected in mainland France in 1999 and the isolate collected from the Reunion Island, as well as German and American RHDV variants. Multiple sequence alignments of the VP60 gene and antigenic analysis with monoclonal antibodies demonstrated that these French isolates are two new isolates of the RHDV variant. Received June 7, 2002; accepted August 12, 2002     

Phylogenetic analysis of rabbit haemorrhagic disease virus (RHDV) strains isolated between 1988 and 2003 in eastern Hungary

Summary. To define the genetic variability of RHDV strains collected in eastern Hungary, liver samples from rabbits that had died of RHD were collected between 1988 and 2003. The phylogenetic analysis of a 528-nucleotide-long portion of the gene encoding the VP60 capsid protein assigned the strains into three genogroups. The first group contained viruses from 1988–1993, and a second group comprised isolates from 1994–2002. A third group comprised all of the tested representatives of the RHDVa subtype and a Hungarian isolate from 2003. These findings were supported by the alignments of the deduced amino acid sequences of the VP60 gene and strongly suggest the presence of the RHDVa subtype in Hungary.     

Phylogenetic analysis of swine fever virus strains

Amplification of H-gene fragment in combination with cDNA nucleotide sequencing can be used for indication and strain differentiation of classical swine fever virus.     

Phylogenetic analysis of porcine epidemic diarrhea virus field strains prevailing recently in China

Porcine epidemic diarrhea virus (PEDV) is the causative agent of porcine epidemic diarrhea (PED), which is characterized by severe diarrhea, dehydration and high mortality in the affected pigs. Recently, clinical outbreaks of diarrhea in suckling piglets emerged in pig-producing areas of China. In this study, molecular detection of PEDV was conducted using RT-PCR (targeting the M gene) on samples collected from piglets with watery diarrhea from 15 pig farms, and phylogenetic analysis of PEDV field strains was carried out based on their M and S genes. In addition, the complete genome sequence of a PEDV field strain was determined. PEDV was detected in 92.7 % of the samples (267/288). The 15 M genes that were amplified shared 99.6-100 % nucleotide identity and 99.1-100 % amino acid similarity with each other. The 15 S genes exhibited 98.6-99.9 % homology, both at the nucleotide level and at the deduced amino acid level. Phylogenetic analysis showed that all of the amplified M genes grouped in cluster 3, together with some Chinese, Korean and Thai strains, while all of the amplified S genes were in cluster 3 and were closely related to Korean strains. Compared with previous PEDV strains, all of the S genes have common characteristics, namely, a 4-aa (GENQ) insertion between positions 55 and 56, a 1-aa (N) insertion between positions 135 and 136, and a 2-aa (DG) deletion between positions 155 and 156, similar or identical to Korean KNU-serial strains reported in recent years. The genome of the sequenced PEDV field strain is 28,038 nucleotides in length, excluding the poly (A) tail. Our findings suggest that a novel PEDV with a characteristic variant S gene is responsible for recent outbreaks of clinical diarrhea in piglets in China.     

An immunological method to determine antigenic variation in three strains of myxoma virus

A technique is described for the purification of soluble antigens of three strains of myxoma virus. Radioimmunoassays were used to study the antigenic differences between the three strains. Results show that the soluble antigens isolated from Lu and G.V. strains do not cross-react in rabbits tested, suggesting that rabbits infected with Lu and G.V. strains of the myxoma virus can be readily distinguished. Antigen isolated from the U.F.S. strain cross-reacted with sera from both Lu- and G.V.-infected rabbits.     

Isolation and identification of a non-haemagglutinating strain of rabbit hemorrhagic disease virus from China and sequence analysis for the VP60 Gene

A variant strain of rabbit hemorrhagic disease virus, designated “whn-1”, was isolated and identified in China. The virus lacked haemagglutinating activity at 25, 37 and 4°C, respectively, and gave negative results in the HAT after two passages in experimentally infected rabbits, but gave positive results in Agar Diffusion Reaction (ADR) and Counter Immunoelectrophoresis (CIE). Using electron microscopy, negatively stained particles of the RHDV isolate showed that the virions was approximately 35 nm in diameter. The capsid protein VP60 gene of whn-1 strain was cloned into pMD18-T vector by RT-PCR assays and sequenced. The obtained VP60 gene sequence has been submitted to GenBank with the accession number: DQ069280. The whole VP60 gene of whn-1 was 1740 nt in size and encodes 579 aa. Alignment with other 16 strains of RHDV in the world, including such “RHDVa” strains as France 99-05, France-Reu-00, Germany-Triptis and ChinaTP, in addition to RCV and EBHSV, showed that the homology of RHDV strains were 90.0–98.0% for nucleotide sequence, 94.3–99.0% for amino acid sequence, respectively. The results indicated that the sequences of VP60 gene of different RHDV isolates, including non-haemagglutinating whn-1 strain and low-haemagglutinating Rainham strain, were relatively highly homologous, and the major variant amino acid were located within region C (301–328 aa) and region E(344–434 aa), which were specific to “RHDVa” strains. Moreover, the molecular characterisation of VP60 protein of RHDV whn-1 strain, such as Hydrophilicity plot, Flexible regions, Antigenic index, etc., were compared with reference RHDV strains of Spanish-AST/89, France-99-5 and UK-Rainham in this article. From the experiment, it’s concluded that, the “whn-1” strain is probably an antigenic variant of “RHDVa”, and the 3 amino acids of Phe (304), Ala (305), Ser (309), and 5 amino acids of Gly (359), Asn (365), Ala (369), Ala (370), Asn (386), located in P2 region in the VP60 protein, probably played an important role in the haemagglutination activity.     

Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan

Summary To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). Among them, three major genetic groups were associated with the recent outbreaks of IB in Japan. One group is indigenous to Japan and could not be placed within the known existing groups in other countries. The remaining two groups, which have emerged recently, are related to isolates in China and Taiwan.     

Sequence and genomic organization of a rabbit hemorrhagic disease virus isolated from a wild rabbit

Rabbit hemorrhagic disease virus (RHDV) is a member of the caliciviridae family. The nucleotidic sequence of a full-length cDNA of one RHDV isolate (RHDV-SD) is reported. The genome is 7437 bases long and includes two ORFs, ORF1 (7034 b) and ORF2 (353 b), coding for the polyprotein and the Vp12, respectively. The coding sequence for the second structural protein (the capsid protein, Vp60) is located at the 3 end of ORF1. Comparison of RHDV-SD with the German RHDV isolate revealed 470 nucleotide substitutions (96% homology). The deduced amino acid sequences of the two isolates are closely related (98% identity), and no hypervariable region could be identified either in the structural or nonstructural proteins.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number Z29514.     

Genetic analysis of HAV strains in Tunisia reveals two new antigenic variants

To evaluate the genetic variability of hepatitis A virus (HAV) isolates in Tunisia, serum samples were collected from 99 patients in different Tunisian areas in 2003 containing 92 cases with acute hepatitis, five with severe acute hepatitis and two with fulminant hepatitis. The entire VP1 gene was amplified and sequenced. Sequences were then aligned and a phylogenetic analysis was performed. Additionally, the amino acid (aa) sequence of the VP1 was determined. The analysis of Tunisian HAV isolates revealed that all the isolates were sub-genotype IA with 96.4%–99.8% of identity and showed the emergence of two novel antigenic variants. The Tun31-03 antigenic variant, with a 38 aa deletion containing Met156, Val171, Leu174 and Ala176 and located between 150 and 187 aa of the VP1 protein where neutralization escape mutations, was found. The second antigenic variant, Tun36-03, was isolated from a patient with fulminant hepatitis and presented a substitution of Thr by Pro at position 10 of the VP1 protein. This amino acid is located in a peptide presenting an antigenically reactive epitope of the VP1 protein. This substitution has never been described previously.     

Macrophage tropism of rabbit hemorrhagic disease virus is associated with vascular pathology

To delineate the interactions between rabbit hemorrhagic disease virus (RHDV) and host cells, organ and cellular targets of infection were identified in vivo. Viral specific antigens were detected by immunohistochemistry in liver, lung, spleen and lymph nodes cells. Also, intravascular infected cells were detected in most organs including kidneys, myocardium, thymus and central nervous system. To further characterize infected target cells, viral proteins and cell-specific surface antigens were identified simultaneously in double labeling experiments. Numerous lymphoid organ macrophages, from the splenic red pulp, circulating monocytes, alveolar macrophages and Kupffer cells were double labeled, demonstrating that cells of the mononuclear phagocyte lineage are major hosts for RHDV. Double labeling for other specific cell markers were negative. The distribution of viral antigens in these tissues coincided with those areas where cells presented morphology of apoptosis. Association of intravascular monocyte infection and apoptosis, could represent a possible mechanism to develop disseminated intravascular coagulation.     

Analysis of intratypic variation evident in an Ibaraki virus strain and its epizootic hemorrhagic disease virus serogroup

A new strain of Ibaraki virus (IBAV) was isolated from cattle showing atypical symptoms of Ibaraki disease. The isolate was genetically characterized, and the genetic diversity and evolution of the capsid proteins of viruses in the epizootic hemorrhagic disease virus (EHDV) serogroup were investigated. The nucleotide sequences of the isolate's viral RNA segments 2, 3, 6, and 7, which encode the viral structural proteins VP2, VP3, VP5, and VP7, respectively, were determined and were then compared against those of the existing strains of IBAV and EHDV, to which IBAV belongs serologically. The nucleotide sequences of segments 3 and 7 were conserved within the EHDV serogroup, particularly well among the strains of IBAV and Australian EHDV. The similarity of the sequence of segment 6 of the isolate to sequences of corresponding segments of the other strains of IBAV and EHDV was found to be about 93%. The similarity of segment 2 of the isolate to segments 2 of the other strains of IBAV and EHDV was less than 70%. Phylogenetic analysis based on the deduced amino acid sequences of segments 3 and 7 revealed that the viruses differed according to their geographical distributions. However, the new isolate of IBAV was categorized as having a distinct lineage in the phylogenetic tree of VP2. These results suggest that the isolate was modified by a reassortment of segment 2 and that it exhibits unique genetic and antigenic characteristics.     

Limited antigenic variation among recent infectious bursal disease virus isolates from France

Summary.  Seven neutralizing monoclonal antibodies (Mabs) to infectious bursal disease virus (IBDV) were used in an antigen-capture ELISA for the antigenic characterization of 58 IBDV isolates obtained in France since 1989. Fifty-six isolates exhibited an antigenic profile which was different from reference strain Faragher 52/70, and similar to French very virulent IBDV strain 89 163 (no binding of two Mabs). Two strains (3.4%), isolated in 1991 and 1994, showed additional antigenic modifications resulting in suppressed or reduced binding activity of three other Mabs. The two atypical viruses were not re-identified in field samples subsequently collected, hence showing that antigenic variants of IBDV do not tend to replace the antigenically dominant 89 163-like strains that have prevailed in France since 1989. Received March 14, 1997 Accepted June 2, 1997     

SEN病毒ORF2基因序列和抗原性的初步分析

目的对SEN病毒(SENV)开放阅读框(ORF)2基因进行序列测定分析和原核表达,并对表达蛋白进行抗原性分析。方法用聚合酶链反应(PCR)方法扩增SENVORF2基因,对该基因进行序列测定、系统进化分析,双酶切扩增产物与原核表达载体pRSETB构建成重组质粒,诱导表达后进行SDSPAGE和免疫印迹分析。结果该株SENVORF2与北京株(AY072045)核苷酸同源性为97%,氨基酸同源性为59%;与日本株(AB059352)同源性分别为90%和56%。含有SENVORF2质粒的菌株表达相对分子质量约为19×103的融合蛋白,免疫印迹证明该融合蛋白能与SENVDNA阳性血清发生特异反应。结论表达了158个氨基酸的SENVORF2原核表达蛋白具有一定的抗原活性。     

Genetic analysis of the M RNA segment of Crimean-Congo hemorrhagic fever virus strains in Turkey

Summary Crimean-Congo hemorrhagic fever (CCHF) virus is member of the genus Nairovirus of the family Bunyaviridae. All members of the family Bunyaviridae are enveloped viruses containing tripartite, negative polarity, single-stranded RNA. CCHF is characterized by high case mortality, occurring in Asia, Africa, the Middle East and Europe. During recent years, outbreaks have been reported in Turkey. However, little information is available on the genetic diversity of CCHF virus in Turkey. In this study, a total of 1227 adult ticks were collected from domestic ruminants (796 specimens from cattle, 399 specimens from goats and 32 specimens from sheep). The presence of the M segment of CCHF virus was determined in 4 of 40 (10%) Hyalomma marginatum marginatum pools, in 2 of 38 (7.89%) Rhipicephalus bursa pools, and in 1 of 7 (7%) Boophylus annulatus pools. Hyalomma anatolicum anatolicum pools gave negative RT-PCR result against CCHF virus. Serum samples from seven patients infected with CCHF were selected and subjected to RT-PCR to amplify partial M segment of CCHF virus. This report introduces the first data on partial nucleotide sequences of M RNA segments of CCHF virus strains circulating in Turkey, isolated from ticks. Correspondence: Aykut Ozdarendeli, Department of Virology, Firat University College of Veterinary Medicine, 23119 Elazig, Turkey     

Antigenic variation in rabies virus strains

Several rabies virus isolates from small wild rodents, one strain isolated from a fox and another from a cat, as well as the CVS strain were compared in cross-protection and virus-neutralization tests. Antigenic variations between the strains and between different batches of individual strains were found. These antigenic differences could not be explained by denaturation caused by UV irradiation or deep-freeze storage, by the presence of "incomplete" particles or by passage in immune organism. An antigenic difference was batch-specific and was only demonstrable on comparison with a relatively large number of strains: it has probably developed during the assembly of antigenic determinants of the virion. There was no correlation between protective and virus-neutralizing activities.     

Variabilities in the antigenic structure of persisting tick-borne encephalitis virus strains

Antigenic variants in the E protein from persisting tick-borne encephalitis (TBE) virus strains were analyzed using monoclonal antibodies (MAbs) to an analogous protein of the reference Sofyin strain. MAbs to sequential epitopes demonstrated their ability to differentiate persisting TBE virus strains from Sofyin and from each other. Two MAbs (2H3 and 13D6) showed a higher neutralizing activity in the interaction with persisting TBE virus variants as compared to the Sofyin strain. Based on the obtained data, a comparison was made of topologically identical epitopes from the E protein of reference and persisting virus strains. The possibility of increasing the neutralizing activity of MAbs through alterations in the primary structure of sequential antigenic sites is discussed.