Whole-genome sequence analysis of a novel orthobunyavirus isolated in Japan in the 1980s.

Two viruses isolated from Culicoides biting midges in Japan and preserved in a frozen state for over three decades were genetically characterized by next-generation sequencing. The viruses have a tripartite RNA genome with the typical coding strategy of orthobunyaviruses. They also share a high level of genetic similarity and are thus regarded as isolates of the same virus. Pairwise sequence comparisons and phylogenetic analysis including viruses of the Simbu serogroup demonstrated that the new viruses are members of clade A of this serogroup. In addition, a discrepancy in the phylogenetic trees indicated that a genetic reassortment had occurred in the evolution of the studied viruses. The L protein of the virus reported here showed no more than 94.6% amino acid sequence identity to that of any other Simbu serogroup virus, indicating that it should be regarded as a novel virus according to a criterion for species definition in the genus Orthobunyavirus. Therefore, this novel virus is tentatively named 'Taniyama virus' based on the location where the infected midges were collected.

Simbu Viruses' Infection of Livestock in Israel-A Transient Climatic Land.

Important lessons have been learned by the Israeli veterinary community regarding Simbu serogroup viruses infections. This serogroup of viruses might cause the births of neonatal malformation in susceptible ruminant's populations. Until 2012, only Akabane virus was connected with the births of malformed ruminants in Israel. However, serological and genomic detection tests, coupled with viral isolations, revealed that more than a single Simbu serogroup serotype could be present concurrently in the same farm or even in the same animal. From 2012 to date, Aino, Shuni, Shamunda, Satuperi, Peaton, Schmallenberg, and Sango viruses have been found in Israel either by serological or genomic investigation. Israel is located in the Eastern Mediterranean Basin, a terrestrial and climatic bridge between the three old continents. The Eastern Mediterranean shores benefit from both the tropical/subtropical and the continental climatic conditions. Therefore, the Eastern Mediterranean basin might serve as an optimal investigatory compound for several arboviral diseases, acting as a sentinel. This review summarizes updated information related to the presence of Simbu serogroup viruses in Israel.

Evolutionary history of Simbu serogroup orthobunyaviruses in the Australian episystem.

Orthobunyaviruses of the Simbu serogroup are transmitted by insects (primarily biting midges) and infect mammals and/or birds. Many have been associated with disease in livestock or humans. The orthobunyavirus genome comprises three negative-sense RNA segments (L, M and S). We report the complete coding sequences of 57 isolates of Simbu serogroup viruses collected in Australia during 1968-1984. Phylogenetic analysis identified novel genogroups of Akabane virus (AKAV), Aino virus (AINOV) and Peaton virus, and provided evidence of constrained movement of AKAV between epidemiological systems in the northern and eastern regions of the continent. Differential clustering of AKAV isolates in trees inferred from L, M and S segments was indicative of intratypic segment reassortment. Similarly, intertypic segment reassortment was detected between AKAV and Tinaroo virus, and between AINOV and Douglas virus. L segments representing novel genogroups were detected in AINOV reassortants, suggesting the presence of unidentified Simbu group viruses in the episystem.

Serological evidence suggests that several Simbu serogroup viruses circulated in Israel.

Viruses of the Simbu serogroup are arboviruses that are known to cause outbreaks of abortion, stillbirth and congenitally deformed neonates. This study presents the results of antibody screening of Simbu serogroup viruses in heifers born in Israel after October 2013, and in adult milking cows born before May 2012. Thirteen dairy cattle farms in five regions, and one sheep flock, entered this study. Serum samples that were found to be positive by ELISA were further tested by specific virus- neutralization test against a panel of Simbu serogroup viruses including Akabane, Aino, Sathuperi, Shamonda, and Peaton viruses. Antibody detection in lactating adult cows revealed that several viruses were circulating in Israel between 2008-2014. Moreover, during autumn 2014 the heifers became serum-positive after being exposed to more than one Simbu serogroup virus concurrently. The results of this study shed new light on Simbu virus infections in Israel, and may contribute to the epidemiology of the Simbu serogroup around the Mediterranean Basin in general.

First genomic detection of Peaton virus in a calf with hydranencephaly in Israel.

Simbu serogroup are arbo- viruses which are mainly transmitted by Culicoides. Two members of the Simbu serogroup, Akabane and Shuni viruses, have been isolated from congenitally malformed ruminants in Israel. A recent serosurvey revealed that Israeli ruminants have been exposed to several additional Simbu viruses, including Shamonda and Sathuperi that seems to be circulating in Israel. In April 2017, an apparently healthy one-month-old male calf was transferred to the Kimron Veterinary Institute. A few days later, the calf was reported to be slow to respond to its surroundings and was not able to feed on its own. Blindness was observed upon clinical examination. RNA of the small, medium and large segments of Simbu serogroup viruses were amplified and sequenced from the testis tissues and from the Cerebrospinal fluid (CSF). During post-mortem examination, hydranencephaly was defined. Phylogenetic analysis of all three segments of Simbu serogroup viruses showed that the sequences detected in the Israeli calf were virtually identical to Peaton virus (PEAV). PEAV was also detected in two pools of Culicoides imicola trapped at two different locations in Israel. This is the first genomic detection of PEAV outside Australia and Japan. These results are of epidemiological significance, as they demonstrate that PEAV is circulating in Israel and affects cattle. Consequently, these results are also of relevance to a potential spread of Simbu serogroup viruses into Europe.

Characterization of Unknown Orthobunya-Like Viruses from India.

Next-generation sequencing (NGS) of agents causing idiopathic human diseases has been crucial in the identification of novel viruses. This study describes the isolation and characterization of two novel orthobunyaviruses obtained from a jungle myna and a paddy bird from Karnataka State, India. Using an NGS approach, these isolates were classified as Cat Que and Balagodu viruses belonging to the Manzanilla clade of the Simbu serogroup. Closely related viruses in the Manzanilla clade have been isolated from mosquitos, humans, birds, and pigs across a wide geographic region. Since Orthobunyaviruses exhibit high reassortment frequency and can cause acute, self-limiting febrile illness, these data suggest that human and livestock infections of the Oya/Cat Que/Manzanilla virus may be more widespread and/or under-reported than anticipated. It therefore becomes imperative to identify novel and unknown viruses in order to understand their role in human and animal pathogenesis. The current study is a step forward in this regard and would act as a prototype method for isolation, identification and detection of several other emerging viruses.

Development and validation of a universal S-segment-based real-time RT-PCR assay for the detection of Simbu serogroup viruses.

Simbu serogroup viruses induce acute clinical diseases and abnormal courses of pregnancies in livestock. In Israel, two members of this serogroup, namely Akabane virus (AKAV) and Shuni virus (SHUV), were recently detected and, in Europe, Schmallenberg virus (SBV) poses a threat to ruminants. To address this emerging problem, a universal S-segment-based real-time RT-PCR assay (Uni-S) for the detection of Simbu serogroup viruses was established, which, additionally, enabled species identification of the detected viruses by subsequent sequencing. The newly developed probe-based PCR system enabled reliable detection of a comprehensive panel of Simbu viruses. Furthermore, several SBV isolates and German field samples were tested by the new Uni-S system in comparison to a SBV-specific real-time RT-PCR and both assays exhibited equally high levels of sensitivities. Finally, co-circulation of AKAV and SHUV in Israel was confirmed by analyzing field samples using the Uni-S assay followed by sequence analysis of the positive samples. To validate the test specificity, blood and tissue samples from animals negative for Simbu viruses, preparations of genetically related viruses and additional ruminant pathogens were examined and all were found to be negative. In conclusion, the new assay enabled sensitive and rapid universal molecular detection of Simbu viruses and is expected to serve as a valuable method for infection diagnosis, especially in regions where several Simbu serogroup members circulate.

Congenital Malformations of Calves Infected with Shamonda Virus, Southern Japan.

In 2015 and 2016, we observed 15 malformed calves that were exposed to intrauterine infection with Shamonda virus, a Simbu serogroup orthobunyavirus, in Japan. Characteristic manifestations were arthrogryposis and gross lesions in the central nervous system. Our results indicate that this arbovirus should be considered a teratogenic virus in ruminants.

Isolation and characterization of Oya virus a member of Simbu serogroup, family Bunyaviridae, isolated from Karnataka, India.

During a study on Japanese encephalitis (JE) from Kolar district of Karnataka state, India in 1986; two virus isolates were obtained in infant Swiss albino mouse from a pig and a human serum sample. For characterization of these virus isolates, they were propagated in Vero CCL-81 cells. These virus isolates were screened for flaviviruses (Japanese encephalitis, West Nile, Dengue, Kyasanur forest disease) and Alphavirus (Chikungunya) by RT-PCR and found to be negative. Further these they were screened for bunyaviruses using genus-specific primers. A virus isolate from a human sample was sequenced using next generation sequencing; which identified it as Oya virus, Simbu group of the genus Orthobunyavirus of the family Bunyaviridae. Phylogenetic analysis of L, M, S (N and NSs) revealed its close association with Chinese strain of Oya virus in Simbu serogroup with the distance of 6.5>4.2>3.2% for nucleotides and 2.4>0.8>0.0% for the amino acid of L>M>S segments respectively. Based on the PCR results; an isolate from pig sample was also confirmed as Oya virus. This study was strengthened by findings of IgG antibody positivity against Oya virus in retrospective serum samples of suspected febrile illness cases from this area by an indigenously developed ELISA. Oya virus positivity was also recorded in human samples collected from Karnataka using nested RT-PCR. This is the first report of the presence of Oya virus in human samples. Further studies are needed to determine disease-causing potential in humans.

Detection of Oropouche virus segment S in patients and inCulex quinquefasciatus in the state of Mato Grosso, Brazil.

This study aimed to investigate the circulation of Orthobunyavirus species in the state of Mato Grosso (MT) Brazil. During a dengue outbreak in 2011/2012, 529 serum samples were collected from patients with acute febrile illness with symptoms for up to five days and 387 pools of female Culex quinquefasciatus captured in 2013 were subjected to nested-reverse transcription-polymerase chain reaction for segment S of the Simbu serogroup followed by nucleotide sequencing and virus isolation in Vero cells. Patients (5/529; 0.9%) from Cuiabá (n = 3), Várzea Grande (n = 1) and Nova Mutum (n = 1) municipalities were positive for the S segment of Oropouche virus (OROV). Additionally, eight/387 Cx. quinquefasciatus pools were positive for the segment, with a minimum infection rate of 2.3. Phylogenetic analysis indicated that all the samples belong to the subgenotype Ia, presenting high homology with OROV strains obtained from humans and animals in the Brazilian Amazon. The present paper reports the first detection of an Orthobunyavirus, possibly OROV, in patients and in Cx. quinquefasciatus mosquitoes in MT. This finding reinforces the notion that arboviruses frequently reported in the Amazon Region circulate sporadically in MT during dengue outbreaks.

Detection of Oropouche virus segment S in patients and inCulex quinquefasciatus in the state of Mato Grosso, Brazil

This study aimed to investigate the circulation of Orthobunyavirus species in the state of Mato Grosso (MT) Brazil. During a dengue outbreak in 2011/2012, 529 serum samples were collected from patients with acute febrile illness with symptoms for up to five days and 387 pools of female Culex quinquefasciatuscaptured in 2013 were subjected to nested-reverse transcription-polymerase chain reaction for segment S of the Simbu serogroup followed by nucleotide sequencing and virus isolation in Vero cells. Patients (5/529; 0.9%) from Cuiabá (n = 3), Várzea Grande (n = 1) and Nova Mutum (n = 1) municipalities were positive for the S segment of Oropouche virus (OROV). Additionally, eight/387 Cx. quinquefasciatuspools were positive for the segment, with a minimum infection rate of 2.3. Phylogenetic analysis indicated that all the samples belong to the subgenotype Ia, presenting high homology with OROV strains obtained from humans and animals in the Brazilian Amazon. The present paper reports the first detection of an Orthobunyavirus, possibly OROV, in patients and in Cx. quinquefasciatus mosquitoes in MT. This finding reinforces the notion that arboviruses frequently reported in the Amazon Region circulate sporadically in MT during dengue outbreaks.

Development of a pan-Simbu real-time reverse transcriptase PCR for the detection of Simbu serogroup viruses and comparison with SBV diagnostic PCR systems.

BACKGROUND: Schmallenberg virus (SBV), a novel orthobunyavirus of the Simbu serogroup, was first identified in October 2011 in dairy cattle in Germany, where it caused fever, diarrhea and a drop in milk yield. Since then, SBV additionally has been detected in adult sheep and goats. Although symptoms of acute infection were not observed, infection during a vulnerable phase of pregnancy caused congenital malformations and stillbirths. In view of the current situation and the possible emergence of further Simbu serogroup members, a pan-Simbu real-time reverse transcriptase (RT) PCR system for the reliable detection of Simbu serogroup viruses should be developed. METHODS: In this study a pan-Simbu real-time RT-PCR system was established and compared to several SBV real-time RT-PCR assays. All PCR-systems were tested using a panel of different Simbu serogroup viruses as well as several field samples from diseased cattle, sheep and goats originating from all over Germany. Several pan-Simbu real-time RT-PCR products were sequenced via Sanger sequencing. Furthermore, in silico analyses were performed to investigate suitability for the detection of further orthobunyaviruses. RESULTS: All tested members of the Simbu serogroup (n = 14) as well as most of the field samples were successfully detected by the pan-Simbu real-time RT-PCR system. The comparison of this intercalating dye assay with different TaqMan probe-based assays developed for SBV diagnostics confirmed the functionality of the pan-Simbu assay for screening purposes. However, the SBV-TaqMan-assay SBV-S3 delivered the highest analytical sensitivity of less than ten copies per reaction for duplex systems including an internal control. In addition, for confirmation of SBV-genome detection the highly specific SBV-M1 assay was established. CONCLUSION: The pan-Simbu real-time RT-PCR system was able to detect all tested members of the Simbu serogroup, most of the SBV field samples as well as three tested Bunyamwera serogroup viruses with a suitable sensitivity. According to in silico analyses, this system seems to be able to detect a broad orthobunyavirus spectrum. As an additional feature of the pan-Simbu real-time RT-PCR system, subsequent species classification via sequencing is feasible. Regarding SBV diagnostics, the performance of the S-segment targeting SBV-S3 assay was superior with respect to the analytical sensitivity.

Characterization of messenger RNA termini in Schmallenberg virus and related Simbuviruses.

Schmallenberg virus (SBV) is an emerging arbovirus infecting ruminants in Europe. SBV belongs to the Bunyaviridae family within the Simbu serogroup. Its genome comprises three segments, small (S), medium (M) and large (L), that together encode six proteins and contain NTRs. NTRs are involved in initiation and termination of transcription and in genome packaging. This study explored the 3' mRNA termini of SBV and related Simbuviruses. In addition, the 5' termini of SBV messenger RNA (mRNA) were characterized. For the three SBV segments, cap-snatching was found to initiate mRNA transcription both in vivo and in vitro. The presence of extraneous nucleotides between host RNA leaders and the viral termini fits with the previously described prime-and-realign theory. At the 3' termini, common features were identified for SBV and related Simbuviruses. However, different patterns were observed for the termini of the three segments from the same virus type.

Schmallenberg virus in Culicoides spp. biting midges, the Netherlands, 2011.

To determine which species of Culicoides biting midges carry Schmallenberg virus (SBV), we assayed midges collected in the Netherlands during autumn 2011. SBV RNA was found in C. scoticus, C. obsoletus sensu stricto, and C. chiopterus. The high proportion of infected midges might explain the rapid spread of SBV throughout Europe.

Schmallenberg virus as possible ancestor of Shamonda virus.

Schmallenberg virus (SBV), an orthobunyavirus of the Simbu serogroup, recently emerged in Europe and has been suggested to be a Shamonda/Sathuperi virus reassortant. Results of full-genome and serologic investigations indicate that SBV belongs to the species Sathuperi virus and is a possible ancestor of the reassortant Shamonda virus.

Reemergence of Oropouche fever, northern Brazil.

Oropouche fever has reemerged in Parauapebas and Porto de Moz municipalities, Pará State, Brazil. Serologic analysis (immunoglobulin M-ELISA) and virus isolation confirmed Oropouche virus (OROV) in both municipalities. Nucleotide sequencing of 2 OROV isolates from each location indicated genotypes I (Parauapebas) and II (Porto de Moz) in Brazil.

Akabane virus in Israel: a new virus lineage.

This report describes the first molecular characterization of Akabane virus (AKAV) in Israel. The virus was recognized by real-time RT-PCR in extracts from Culicoides imicola insects trapped at the Volcani Center located in the center of Israel. This is also the first report on the use of real-time RT-PCR to identify the virus. The quantitative capability of this technique was applied, and it was calculated that the insect extract contains 1.5 x 10(5) copies of the genome segment S. Following amplification of the small (S) genome segment, its nucleotide sequence was determined to have 93.4% identity or greater with the S segment of other AKAV isolates. The deduced amino acid (aa) sequence of the combined nucleocapsid and the non-structural protein showed more than 96.6% identity. Phylogentic trees constructed using the combined deduced nucleocapsid and the non-structural protein aa sequences showed that the Israeli isolate forms a fourth cluster of AKAV, indicating a separate virus lineage. Attempts to isolate the virus by inoculation to Vero cells and by intracerebral inoculation to mice were unsuccessful.

The emergence in Japan of Sathuperi virus, a tropical Simbu serogroup virus of the genus Orthobunyavirus.

In 1999, two viruses were isolated from blood samples of sentinel cattle in the Western part of Japan. The physiochemical and morphological properties of these viruses indicated that they belonged to the family Bunyaviridae. Sequence analysis of the S segment indicates that the two viruses are closely related to Sathuperi virus (SATV). The N-terminal 168 amino acid of the G2 protein of the M segment was highly homologous with that of SATV (98.2%). Given these results, we conclude that the newly isolated viruses are closest to SATV, which was initially isolated in India and Nigeria over 30 years ago.