Molecular characterization of double-stranded RNA segments encoding the major capsid proteins of a Palyam serogroup orbivirus that caused an epizootic of congenital abnormalities in cattle

Development and evaluation of recombinase polymerase amplification combined with lateral flow dipstick assays for co-detection of epizootic haemorrhagic disease virus and the Palyam serogroup virus

Background

Epizootic haemorrhagic disease virus (EHDV) and the Palyam serogroup viruses (PALV) have led to significant economic losses associated with livestock production globally. A rapid, sensitive and specific method for the detection of EHDV and PALV is critical for virus detection, monitoring, and successful control and elimination of related diseases.

Results

In the present study, a recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) assay for the co-detection of genome segment 1 (Seg-1) of EHDV and PALV was developed and evaluated. The analytical sensitivities of the established RPA-LFD assay in the detection of EHDV and PALV were 7.1 copies/µL and 6.8 copies/µL, respectively. No cross-reaction with other members of the genus Orbivirus, including African horse sickness virus, bluetongue virus, Guangxi orbivirus, Tibet orbivirus and Yunnan orbivirus was observed. The established RPA-LFD assay accurately detected 39 EHDV strains belonging to 5 serotypes and 29 PALV strains belonging to 3 serotypes. The trace back results of quantitative real-time polymerase chain reaction (qRT-PCR) and the established RPA-LFD assay on sentinel cattle were consistent. The coincidence rates of qRT-PCR and the established RPA-LFD assay in 56 blood samples from which EHDV or PALV had been isolated and 96 blood samples collected from cattle farms were more than 94.8 %. The results demonstrated that the established RPR-LFD assay is specific, sensitive and reliable, and could be applied in early clinical diagnosis of EHDV and PALV.

Conclusions

This study highlights the development and application of the RPA-LFD assay in the co-detection of EHDV and PALV for the first time. The assay could be used as a potential optional rapid, reliable, sensitive and low-cost method for field diagnosis of EHDV and PALV.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02977-9.

Phylogenetic Characterization of the Palyam Serogroup Orbiviruses

The Palyam serogroup orbiviruses are associated with abortion and teratogenesis in cattle and other ruminants. Of the 13 different serotypes that have been identified, the full genome sequence of only one, Kasba, has been published. We undertook to perform Next Generation Sequencing (NGS) and phylogenetic analysis on 12 Palyam serotypes plus field isolates of the African serotypes in our possession. The Palyam serogroup was found to be most closely related to the African horse sickness virus group and showed the most distant evolutionary relationship to the equine encephalosis viruses (EEV). Amino acid sequence analysis revealed that the gene encoding VP7 was the most conserved within serotypes and VP2 and VP5 showed the highest degree of variation. A high degree of sequence identity was found for isolates from the same geographical region. The phylogenetic analysis revealed two clades where the African serotypes were all very closely related in one clade and the other clade contained the Australian and Asian serotypes and one African serotype, Petevo. It was evident from the sequence data that the geographical origin of Palyam serogroup viruses played an important role in the development of the different serotypes.

Isolation, complete genome sequencing, and phylogenetic analysis of the first Chuzan virus in China

A Chuzan virus (CHUV), defined as GX871 here, was isolated from blood from a sentinel cattle firstly in China, and its full-length genome was sequenced in this study. The GX871 genome included 10 segments and 18914 bp, one base fewer than the CHUV prototype strain K-47 due to a one-base deletion in the 5' non-coding region of segment 8. A frameshift mutation was detected in a short coding region (1010-1026 nt) corresponding to the VP1 protein; this frameshift resulted in a five-amino acid mutation from 336CVLSY340 to 336YGAKL340. In addition, there were a one-base deletion at 1713 nt and a one-base insertion at 1682 nt in the 3' non-coding region of segment 5. Based on phylogenetic analysis of the deduced VP2 amino acid sequences, Palyam serogroup viruses were classified into three groups. The Chinese CHUV isolate GX871 was categorized into the same group as CHUV prototype strain K-47. The phylogenetic tree was divided into three clusters according to the geographical distribution of the partial nucleotide sequences of VP7, and this arrangement might define the geographical gene pool of CHUV.

Complete genome sequence of a Chuzan virus strain isolated for the first time in mainland China

Chuzan virus (CHUV) belongs to the Palyam serogroup, causes bovine congenital disease, and is prevalent in Asia. To date, only one full Palyam virus (PALV) genome sequence, that of Japanese CHUV strain K47, has been reported. Sequence analysis indicates that PALV strains isolated from different geographical regions show significant diversity, which is mainly shaped by geographically independent evolution and genetic reassortment. Our understanding of the genetic characteristics of PALV is hampered by a very limited genomic sequence database. In this study, we report the complete genome sequence of CHUV strain SZ187, which was isolated for the first time in 2012 in mainland China. Sequence alignment and phylogenetic analysis demonstrate that SZ187 is closely related to other CHUV strains isolated in Taiwan and Japan, indicating that they may share a common ancestor. This new full-length CHUV genome sequence could help in the design of broader assays for epidemiological studies and facilitate the identification of new CHUV isolates in the future.

Development of inactivated trivalent vaccine for the teratogenic Aino, Akabane and Chuzan viruses

Aino, Akabane and Chuzan viruses are arthropod-borne (arbo) viruses transmitted by blood-sucking insects like mosquitoes and Culicoides biting midges. These arbovirus infections are mainly associated with abortion, stillbirth and congenital defects in pregnant cattle, sheep and goats, which induces a considerable economic loss in livestock industry. The viruses seem to be widely distributed in Southeast Asia and Australia. As a control strategy, an inactivated trivalent vaccine against Aino, Akabane and Chuzan virus was developed by using binary ethylenimine or formalin as an inactivating agent. The newly developed trivalent vaccine is evaluated for its safety and immunogenicity in animals such as mice, guinea pigs and cattle. The immune responses were significantly detected within 2-weeks after second vaccination without any side effects. Since the field application of experimental vaccine also revealed increased antibodies in inoculated cattle, we demonstrated that these trivalent vaccines could be used as a vaccine to control the arboviral infections in ruminants.

A single-tube RT-PCR for rapid detection and differentiation of some African isolates of palyam serogroup orbiviruses

A single-tube nested reverse transcriptase (nRT) polymerase chain reaction (nRT-PCR) was developed and evaluated for detection of palyam serogroup orbiviruses ribonucleic acid (RNA) in cell cultures and clinical samples. A pair of outer primers (pal1 and pal2), designed from genome segment three of Chuzan virus of the palyam viruses serogroup, resulted in amplification of a primary 660-base pair (bp) PCR product. Using a pair of internal (nested) primers (pal3 and pal4), the nRT-PCR produced a 350-bp PCR product. The primary and the nested PCR products were amplified from RNA extracted from Sudanese and South African isolates of palyam viruses, propagated in cell cultures. Application of this nRT-PCR to clinical samples resulted in direct detection of palyam virus RNA in blood and serum samples from infected cattle and goats. The nested amplification increased the sensitivity of the assay by 1000-fold, and specific PCR products were detected from as little as 0.1fg of viral RNA. Amplification products were not detected when the nRT-PCR was applied to RNA from closely related orbiviruses including, bluetongue virus (BTV) serotypes 1, 2, 4, 6; epizootic hemorrhagic disease of deer virus prototype serotype 1 (EHDV-1); Sudanese isolates of EHDV-318; total nucleic acid extracts from non-infected Vero cells; and blood and sera from goats and calves from which virus was not isolated. This nRT-PCR provides a reliable, sensitive and specific assay for rapid detection and differentiation of palyam viruses from other related orbiviruses. In addition, the assay is recommended for inclusion in epidemiological surveys and during investigation of an epizootic of the disease among susceptible ruminants.

Sero-survey on Aino, Akabane, Chuzan, bovine ephemeral fever and Japanese encephalitis virus of cattle and swine in Korea

Vector-borne arboviruses produce mild to severe symptoms in domestic animals. Bovine ephemeral fever (BEF), Akabane, Aino, and Chuzan virus have been primarily attributed to reproductive disorders or febrile diseases in cattle, and Japanese encephalitis virus (JEV) is mainly associated with reproductive failures in swine. We investigated antibody titers from domestic swine against four bovine arboviruses (BEF, Akabane, Aino, and Chuzan virus) and from cattle against JEV in Korea. While the positive rates for Akabane and BEF were 37.4% and 15.7%, the positive incidence of Chuzan and Aino were relatively low, with positive rates of 3.04% and 0.4%, respectively, based on a virus neutralization assay. Antibody titers against more than one virus were also frequently detected in domestic swine. The incidence of JEV was 51.3% among domestic cattle. In addition, one positive case was detected in the thoracic fluids from 35 aborted calves, based on the hemagglutination inhibition test. Our results indicate that swine are susceptible hosts of bovine arboviruses without showing clinical symptoms in a natural environment. Moreover, we confirmed that JEV could be associated with reproductive failure in pregnant cattle, as were other vector-borne bovine arboviruses assessed in this study.

Analysis and phylogenetic comparisons of full-length VP2 genes of the 24 bluetongue virus serotypes

The outer capsid protein VP2 of Bluetongue virus (BTV) is a target for the protective immune response generated by the mammalian host. VP2 contains the majority of epitopes that are recognized by neutralizing antibodies and is therefore also the primary determinant of BTV serotype. Full-length cDNA copies of genome segment 2 (Seg-2, which encodes VP2) from the reference strains of each of the 24 BTV serotypes were synthesized, cloned and sequenced. This represents the first complete set of full-length BTV VP2 genes (from the 24 serotypes) that has been analysed. Each Seg-2 has a single open reading frame, with short inverted repeats adjacent to conserved terminal hexanucleotide sequences. These data demonstrated overall inter-serotype variations in Seg-2 of 29 % (BTV-8 and BTV-18) to 59 % (BTV-16 and BTV-22), while the deduced amino acid sequence of VP2 varied from 22.4 % (BTV-4 and BTV-20) to 73 % (BTV-6 and BTV-22). Ten distinct Seg-2 lineages (nucleotypes) were detected, with greatest sequence similarities between those serotypes that had previously been reported as serologically ‘related’. Fewer similarities were observed between different serotypes in regions of VP2 that have been reported as antigenically important, suggesting that they may play a role in the neutralizing antibody response. The data presented form an initial basis for BTV serotype identification by sequence analyses and comparison of Seg-2, and for development of molecular diagnostic assays for individual BTV serotypes (by RT-PCR).

Evidence of an antigenic shift among Palyam serogroup orbiviruses

The Japanese isolates of Palyam serogroup viruses isolated from 1985 to 2001 were investigated for the genome sequence of segments 2 and 7 and were phylogenetically analyzed in comparison with Australian and African isolates of the same serogroup. The nucleotide sequences of segment 7 were highly conserved within Japanese isolates (95.1 to 100%) and between Japanese and Taiwanese isolates (96.0 to 100%), whereas the identities between Japanese and Taiwanese isolates and Australian and African isolates were fairly conserved (84.2 to 92.0%). Phylogenetic analysis based on segment 7 revealed three clusters according to geographical origin. As a result of the nucleotide sequence analysis of segment 2, which encodes a serotype-specific antigen, Japanese isolates were classified into two groups by genome length and nucleotide identities. Four of the nine Japanese isolates were categorized into the same group as prototype strain K-47 of the Chuzan virus, and the remaining isolates were categorized into the same group as the D'Aguilar virus and Nyabira virus. Phylogenetic analysis based on segment 2 revealed two clusters, the cluster containing Chuzan virus and the cluster containing the D'Aguilar and Nyabira viruses. To examine the antigenic relationship among viruses categorized in different clusters, we conducted a cross-neutralization test. KSB-29/E/01, isolated in 2001 in Japan, was neutralized by antiserum not only to strain B8112 of D'Aguilar virus but also to Chuzan virus. These results indicated that genetically and antigenically unique characteristics of KSB-29/E/01 were attributed to genetic reassortment of segment 2 between Chuzan virus and D'Aguilar virus.

Cloning and sequence analysis of dsRNA segments 5, 6 and 7 of a novel non-group A, B, C adult rotavirus that caused an outbreak of gastroenteritis in China

A diarrhoeal outbreak among adults in China was caused by a new rotavirus, termed ADRV-N, that does not react with antisera directed against group A, B or C rotaviruses [Zhonghua Liu Xing Bing Xue Za Zhi (Chin. Epidemiol.) 19 (1998) 336]. ADRV-N can be propagated in cell cultures [Zhonghua Yi Xue Za Zhi (Natl. Med. J. China) 82 (2002) 14]. We present the complete sequences for ADRV-N genome segments 5 and 6, and a full ORF sequence of genome segment 7. The deduced amino acid sequences suggest that these segments encode NSP1, VP6 and NSP3, respectively. These three ADRV-N genome segments have a unique -ACCCC-3' terminal sequence. The 5'-GG- terminus of segments 5 and 6 is the same as that of other rotaviruses. The amino acid similarity between VP6 and NSP3 of ADRV-N and the cognate sequences of their closest counterpart, group B IDIR, was 37 and 35%, respectively. The ADRV-N NSP1 has a double-stranded RNA binding motif (DSRM) and a putative autoproteolytic cleavage motif upstream from the DSRM. The putative ADRV-N NSP3 has a truncated C-terminus compared to the cognate protein of group B rotaviruses. All the available data demonstrate that ADRV-N differs significantly from the known rotaviruses and strongly suggest that ADRV-N is the first recognized member of a new group of rotaviruses infecting humans.

Development of competitive ELISA for serodiagnosis on African horsesickness virus using baculovirus expressed VP7 and monoclonal antibody

VP7, the sero-group common antigen, of African horsesickness virus (AHSV-4) was expressed in insect cells by recombinant baculovirus. To develop a specific diagnostic method, monoclonal antibody (Mab) against VP7 was prepared and investigated as diagnostic reagent with the baculovirus expressed VP7. However, the Mab against VP7 of AHSV cross-reacted with Chuzan virus by the indirect immunofluorescence assay (IFA), confirming the presence of conserved domain of VP7 among Orbiviruses. This study describes two types of ELISA; Mab linked indirect (I-ELISA) and competitive-ELISA (C-ELISA) using baculovirus expressed VP7 as an antigen. These ELISAs were compared for serodiagnosis of AHSV showing that C-ELISA was more specific than I-ELISA. The results indicated that C-ELISA is applicable to serodiagnosis of AHSV regardless of serotypes.

Expression and antigenic characterization of the major core protein VP7 of Chuzan virus, a member of the Palyam serogroup orbiviruses

The Palyam serogroup-specific antigen, VP7, of Chuzan virus strain K-47 was expressed in insect cells by a recombinant baculovirus. The expressed protein appeared as a single band of 38kDa corresponding to the predicted molecular mass of Chuzan virus VP7 by SDS-polyacrylamide gel electrophoresis (SDS-PAGE). In immunoprecipitation analysis, the recombinant VP7 was not only recognized by all polyclonal antibodies against the Palyam serogroup viruses (PALV) tested in this study, but also by antisera to bluetongue virus (BTV) serotype 1, epizootic haemorrhagic disease virus (EHDV) serotypes 1 and 2. However, in Western immunoblot assay, no positive signals were observed between this protein and these antisera, even in the homologous reaction using antiserum to Chuzan virus. These findings demonstrate that the common antigenic determinants on the VP7 proteins of Chuzan virus and the other PALV serotypes are mainly conformational and that the proteins share some epitopes with those of BTV and EHDV beyond the serogroup. No cross-reactivities were detected between Chuzan virus VP7 and antisera to BTV and EHDV in agar gel immunodiffusion (AGID) and indirect ELISA tests, indicating that the recombinant VP7 is useful as a diagnostic reagent for serological tests of congenital abnormalities of cattle caused by PALV.

Genetic diversity of RNA segments 5, 7 and 9 of the Palyam serogroup orbiviruses from Japan, Australia and Zimbabwe

Reverse transcriptase-polymerase chain reaction (RT-PCR) methods, based on the sequences of RNA segments 5, 7 and 9 of Chuzan virus, were established for specific detection and molecular characterization of the Palyam serogroup orbiviruses. Nucleotide sequences obtained from the amplified cDNA fragments of these three genes of 24 isolates were analyzed and compared individually to determine the intra-serogroup phylogenetic relationship of Japanese, Australian and Zimbabwean isolates. It seems that Chuzan virus isolates in Japan are genetically stable. Interestingly, mutations have occurred almost simultaneously on these three genes of Chuzan virus. In all cases, isolates from the same geographical area were closely related to each other at the molecular level, irrespective of serotype. The data suggested that the Palyam serogroup viruses can be differentiated into geographically distinct groups and that the viruses evolve independently in the different gene pools. A strain KY-115 was considered to be produced by reassortment of genome segments between different groups. Restriction fragment length polymorphism (RFLP) analysis of these PCR products is useful for rapid discrimination of isolates and for detection of genetic mutations.