Common occurrence of Belerina virus, a novel paramyxovirus found in Belgian hedgehogs

Discovery and characterization of novel jeilongviruses in wild rodents from Hubei, China

The genus Jeilongvirus comprises non-segmented negative-stranded RNA viruses that are classified within the Paramyxoviridae family by phylogeny. Jeilongviruses are found in various reservoirs, including rodents and bats. Rodents are typical viral reservoirs with diverse spectra and zoonotic potential. Little is currently known about jeilongviruses in rodents from central China. The study utilized high-throughput and Sanger sequencing to obtain jeilongvirus genomes, including those of two novel strains (HBJZ120/CHN/2021 (17,468 nt) and HBJZ157/CHN/2021 (19,143 nt)) and three known viruses (HBXN18/CHN/2021 (19,212 nt), HBJZ10/CHN/2021 (19,700 nt), HBJM106/CHN/2021 (18,871 nt)), which were characterized by genome structure, identity matrix, and phylogenetic analysis. Jeilongviruses were classified into three subclades based on their topology, phylogeny, and hosts. Based on the amino acid sequence identities and phylogenetic analysis of the L protein, HBJZ120/CHN/2021 and HBJZ157/CHN/2021 were found to be strains rather than novel species. Additionally, according to specific polymerase chain reaction screening, the positive percentage of Beilong virus in Hubei was 6.38%, suggesting that Beilong virus, belonging to the Jeilongvirus genus, is likely to be widespread in wild rodents. The identification of novel strains further elucidated the genomic diversity of jeilongviruses. Additionally, the prevalence of jeilongviruses in Hubei, China, was profiled, establishing a foundation for the surveillance and early warning of emerging paramyxoviruses.

Cleavage of the syncytial protein of J paramyxovirus is required for its ability to promote cell-cell fusion

Cell-cell fusion mediated by most paramyxovirus requires fusion protein (F) and attachment protein (H, HN, or G). The F protein is proteolytic cleaved to be fusogenically active. J paramyxovirus (JPV) has a unique feature in the family Paramyxoviridae: It encodes an integral membrane protein, syncytial protein (SP, formerly known as transmembrane protein, TM), which is essential in JPV-promoted cell-cell fusion (i.e., syncytial). In this study, we report that cleavage of SP is essential for its syncytial-promoting activity. We have identified the cleavage site of SP at amino acid residues 172 to 175, LKTG, and deletion of the "LKTG" residues abolished SP protein cleavage and its ability to promote cell-cell fusion. Replacing the cleavage site LKTG with a factor Xa protease cleavage site allows cleavage of the SP with factor Xa protease and restores its ability to promote cell-cell fusion. Furthermore, results from a hemifusion assay indicate that cleavage of SP plays an important role in the progression from the intermediate hemifusion state to a complete fusion. This work indicates that SP has many characteristics of a fusion protein. We propose that SP is likely a cell-cell fusion-promoting protein.

Discovery and genetic characterization of novel paramyxoviruses from small mammals in Hubei Province, Central China

Paramyxoviruses are a group of single-stranded, negative-sense RNA viruses, some of which are responsible for acute human disease, including parainfluenza virus, measles virus, Nipah virus and Hendra virus. In recent years, a large number of novel paramyxoviruses, particularly members of the genus Jeilongvirus, have been discovered in wild mammals, suggesting that the diversity of paramyxoviruses may be underestimated. Here we used hemi-nested reverse transcription PCR to obtain 190 paramyxovirus sequences from 969 small mammals in Hubei Province, Central China. These newly identified paramyxoviruses were classified into four clades: genera Jeilongvirus, Morbillivirus, Henipavirus and Narmovirus, with most of them belonging to the genus Jeilongvirus. Using Illumina sequencing and Sanger sequencing, we successfully recovered six near-full-length genomes with different genomic organizations, revealing the more complex genome content of paramyxoviruses. Co-divergence analysis of jeilongviruses and their known hosts indicates that host-switching occurred more frequently in the evolutionary histories of the genus Jeilongvirus. Together, our findings demonstrate the high prevalence of paramyxoviruses in small mammals, especially jeilongviruses, and highlight the diversity of paramyxoviruses and their genome content, as well as the evolution of jeilongviruses.

Tailam paramyxovirus C protein inhibits viral replication

Jeilongviruses are emerging single-stranded negative-sense RNA viruses in the Paramyxoviridae family. Tailam paramyxovirus (TlmPV) is a Jeilongvirus that was identified in 2011. Very little is known about the mechanisms that regulate viral replication in these newly emerging viruses. Among the non-structural viral proteins of TlmPV, the C protein is predicted to be translated from an open reading frame within the phosphoprotein gene through alternative translation initiation. Though the regulatory roles of C proteins in virus replication of other paramyxoviruses have been reported before, the function of the TlmPV C protein and the relevant molecular mechanisms have not been reported. Here, we show that the C protein is expressed in TlmPV-infected cells and negatively modulates viral RNA replication. The TlmPV C protein interacts with the P protein, negatively impacting the interaction between N and P, resulting in inhibition of viral RNA replication. Deletion mutagenesis studies indicate that the 50 amino-terminal amino acid residues of the C protein are dispensable for its inhibition of virus RNA replication and interaction with the P protein.IMPORTANCETailam paramyxovirus (TlmPV) is a newly identified paramyxovirus belonging to the Jeilongvirus genus, of which little is known. In this work, we confirmed the expression of the C protein in TlmPV-infected cells, assessed its function, and defined a potential mechanism of action. This is the first time that the existence of a Jeilongvirus C protein has been confirmed and its role in viral replication has been reported.

Evolution and ecology of Jeilongvirus among wild rodents and shrews in Singapore

BACKGROUND

Jeilongvirus was proposed as a new genus within the Paramyxoviridae in 2018. The advancement in metagenomic approaches has encouraged multiple reports of Jeilongvirus detection following the initial species discovery, enriching species diversity and host range within the genus. However, Jeilongvirus remains understudied in Singapore, where interfaces between humans and small mammals are plentiful.

METHODS

Here, we utilized metagenomic sequencing for the exploration of viral diversity in small mammal tissues. Upon discovery of Jeilongvirus, molecular screening and full genome sequencing was conducted, with the data used to conduct statistical modelling and phylogenetic analysis.

RESULTS

We report the presence of Jeilongvirus in four species of Singapore wild small mammals, detected in their spleen and kidney. We show that full genomes of three Singapore Jeilongvirus encode for eight ORFs including the small hydrophobic and transmembrane proteins. All generated genomes cluster phylogenetically within the small mammal subclade, but share low genetic similarity with representative Jeilongvirus species. Statistical modelling showed no spatial or temporal patterns and differences among species, life history traits and habitat types.

CONCLUSIONS

This study serves as a basis for understanding dynamics between Jeilongvirus and small mammal hosts in Singapore by displaying the virus generalist nature. In addition, the initial detection can help to invoke improved routine surveillance and detection of circulating pathogens in synanthropic hosts.

Regulation of host gene expression by J paramyxovirus

Paramyxoviruses are negative-sense, single-stranded RNA viruses that are associated with numerous diseases in humans and animals. J paramyxovirus (JPV) was first isolated from moribund mice (Mus musculus) with hemorrhagic lung lesions in Australia in 1972. In 2016, JPV was classified into the newly established genus Jeilongvirus. Novel jeilongviruses are being discovered worldwide in wildlife populations. However, the effects of jeilongvirus infection on host gene expression remains uncharacterized. To address this, cellular RNA from JPV-infected mouse fibroblasts was collected at 2, 4, 8, 12, 16, 24, and 48 hours post-infection (hpi) and were sequenced using single-end 75 base pairs (SE75) sequencing chemistry on an Illumina NextSeq platform. Differentially expressed genes (DEGs) between the virus-infected replicates and mock replicates at each timepoint were identified using the Tophat2-Cufflinks-Cuffdiff protocol. At 2 hpi, 11 DEGs were identified in JPV-infected cells, while 1,837 DEGs were detected at 48 hpi. A GO analysis determined that the genes at the earlier timepoints were involved in interferon responses, while there was a shift towards genes that are involved in antigen processing and presentation processes at the later timepoints. At 48 hpi, a KEGG analysis revealed that many of the DEGs detected were involved in pathways that are important for immune responses. qRT-PCR verified that Rtp4, Ifit3, Mx2, and Stat2 were all upregulated during JPV infection, while G0s2 was downregulated. After JPV infection, the expression of inflammatory and antiviral factors in mouse fibroblasts changes significantly. This study provides crucial insight into the different arms of host immunity that mediate Jeilongvirus infection. Understanding the pathogenic mechanisms of Jeilongvirus will lead to better strategies for the prevention and control of potential diseases that may arise from this group of viruses.

Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals

In the future, zoonotic spillover events are expected to occur more frequently. Consequences of such events have clearly been demonstrated by recent outbreaks of monkeypox, Ebola virus, and the well-known severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Virus discovery has proven to be an important tool in the preparation against viral outbreaks, generating data concerning the diversity, quantity, and ecology of the vertebrate virome. Orthoparamyxoviruses, a subfamily within the Paramyxoviridae, are important biosurveillance targets, since they include several known animal, human, and zoonotic pathogens such as Nipah virus, measles virus, and Hendra virus. During this study, 127 bat samples, thirty-four rodent samples, and seventeen shrew samples originating from Belgium were screened for orthoparamyxovirus presence using nested reverse transcription-polymerase chain reaction assays and nanopore sequencing. We present here the complete genomes of six putative new viral species, belonging to the genera Jeilongvirus and Henipavirus. Characterization of these genomes revealed significant differences in gene composition and organization, both within viruses of the same genus and between viruses of different genera. Remarkably, a previously undetected gene coding for a protein of unknown function was identified in the genome of a putative new Henipavirus. Additionally, phylogenetic analysis of jeilongviruses and henipaviruses reveals a division of both genera into two clades, one consisting of bat-borne viruses and the other consisting of rodent- and shrew-borne viruses, elucidating the need for proper reclassification.

Do Urban Hedgehogs (Erinaceus europaeus) Represent a Relevant Source of Zoonotic Diseases?

Urban fauna is defined as animal species that can live in urban environments. Several species, including the western-European hedgehog (Erinaceus europaeus), have now been identified as part of this urban fauna, becoming permanent residents of parks and gardens in different cities across Europe. Due to the importance that this phenomenon represents for zoonotic disease surveillance, several authors have been conducting zoonotic agents' surveys on hedgehog. The aim of this study is to compare zoonotic diseases' prevalence in hedgehogs in urban environments with those from more rural areas. A systematic review with meta-analysis of twelve studied of zoonotic diseases' (in urban and rural areas of Europe) was therefore conducted for this purpose. Fifteen different zoonoses have been assessed in urban environments and six in rural areas. Anaplasma phagocytophilum was the most prevalent zoonotic agent found in urban habitats (96%). Dermatophytosis shows statistically significant differences between locations (p-value < 0.001), with a higher prevalence in urban Poland (55%; n = 182). Our results suggest further research and a standardized monitoring of different hedgehog populations are essential to understanding the epidemiology of several zoonotic pathogens in different habitat types (urban, rural, natural, industrial, etc.) and preventing possible disease outbreaks.

The C-Terminal 300 Amino Acid Residues of the G Protein and Putative Open Reading Frame X of the G Gene of Tailam Paramyxovirus (TlmPV) Are Not Required for Replication in Tissue Culture Cells

Tailam paramyxovirus (TlmPV) was identified in Sikkim Rats in Hong Kong, China in 2011. Its negative sense RNA genome is similar to J paramyxovirus (JPV) and Beilong paramyxovirus (BeiPV), the prototypes of the recently established genus Jeilongvirus. TlmPV genome is predicted to have eight genes in the order 3'-N-P/V/C-M-F-SH-TM-G/X-L-5'. The predicted size of the TlmPV G protein is 1,052 amino acid (aa) residues and much larger than G proteins of typical paramyxoviruses, which are often less than 800 aa. In addition to G open reading frame (ORF) in the G gene, another ORF, termed ORF-X exists in the G gene transcript. Similar ORF-X exists in JPV and BeiPV G gene, but their expression in virus-infected cells has not been confirmed. In this study, we generated infectious TlmPV using a newly developed reverse genetics system. We have found that the G protein of TlmPV is truncated in cultured cells: stop codons emerged in the G open reading frame, resulting in deletions of amino acid residues beyond residue 732. We have obtained infectious TlmPV lacking the C-terminal 307 aa (rTlmPV-G745) and TlmPV lacking the C-terminal 306 aa and the ORF-X (rTlmPV-GΔ746-X). The recombinant TlmPVs lacking the C-terminal 300 aa reach a higher peak viral titer and have improved genome stability in tissue cultured cells. The work indicates that the C-terminal of the G protein of TlmPV and ORF-X are not required for replication in tissue culture cells, and the deletion of the C-terminal confers a growth advantage in tissue culture cells. IMPORTANCE TlmPV is a member of the recently established genus Jeilongvirus. TlmPV encodes a large G protein and its G gene contains ORF-X. In this work, infectious TlmPV was recovered using reverse genetics. Using this system, we have demonstrated that 300 aa of C-terminal of G and the ORF-X are not required for viral replication in tissue culture cells.

Discovery and characterization of novel paramyxoviruses from bat samples in China

Many paramyxoviruses are responsible for a variety of mild to severe human and animal diseases. Based on the novel discoveries over the past several decades, the family Paramyxoviridae infecting various hosts across the world includes 4 subfamilies, 17 classified genera and 78 species now. However, no systematic surveys of bat paramyxoviruses are available from the Chinese mainland. In this study, 13,064 samples from 54 bat species were collected and a comprehensive paramyxovirus survey was conducted. We obtained 94 new genome sequences distributed across paramyxoviruses from 22 bat species in seven provinces. Bayesian phylodynamic and phylogenetic analyses showed that there were four different lineages in the Jeilongvirus genus. Based on available data, results of host and region switches showed that the bat colony was partial to interior, whereas the rodent colony was exported, and the felines and hedgehogs were most likely the intermediate hosts from Scotophilus spp. rather than rodents. Based on the evolutionary trend, genus Jeilongvirus may have originated from Mus spp. in Australia, then transmitted to bats and rodents in Africa, Asia and Europe, and finally to bats and rodents in America.

2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

α2,3-Linked Sialic Acids Are the Potential Attachment Receptor for Shaan Virus Infection in MARC-145 Cells

Shaan virus (ShaV), a novel species of the genus Jeilongvirus, family Paramyxoviridae, was isolated from an insectivore bat (Miniopterus schreibersii) in Korea in 2016. ShaV particles contain a hemagglutinin-neuraminidase (HN) glycoprotein in their envelope that allows the virus to target cells. Typically, diverse paramyxoviruses with HN glycoprotein are reported to interact predominantly with sialic acids, but there are no studies of receptors for ShaV. In this study, the identification of potential receptors for ShaV was demonstrated using sialidase treatments, glycan microarray, magnetic bead-based virus binding assay, and neuraminidase inhibitor treatments. Pretreatment of MARC-145 cells with sialidase, which cleaves α2,3-linked sialic acids, showed higher inhibition of viral infection than α2,6-linked-specific sialidase. These data were supported by the binding of ShaV to predominantly α2,3-linked sialylated glycans in the screening of sialyl linkage patterns through glycan microarray. To further confirm the direct interaction between ShaV and α2,3-linked sialic acids, ShaV was incubated with α2,3- or α2,6-linked sialylated glycans conjugated to magnetic beads, and binding signals were detected only for α2,3-linked sialylated glycans. In addition, the potential of sialic acids as a receptor was demonstrated by the viral replication inhibitory effect of the neuraminidase inhibitor 2,3-dehydro-2-deoxy-N-acetylneuraminicacid (DANA) in the mature virion release steps. Collectively, these results support that α2,3-linked sialic acids are the potential receptor for ShaV infection in MARC-145 cells. IMPORTANCE Bats host major mammalian paramyxoviruses, and novel paramyxoviruses are increasingly being reported around the world. Shaan virus (ShaV), from the genus Jeilongvirus, family Paramyxoviridae, has a potential attachment glycoprotein, HN. Here, we identify that ShaV binds to sialic acid and demonstrate that α2,3-linked sialic acids are the potential receptor for ShaV infection. The presented data regarding ShaV receptor specificity will enable studies into the viral tropism for the host and contribute to the development of new antiviral strategies targeting viral receptors.

Classification of new morbillivirus and jeilongvirus sequences from bats sampled in Brazil and Malaysia

As part of a broad One Health surveillance effort to detect novel viruses in wildlife and people, we report several paramyxovirus sequences sampled primarily from bats during 2013 and 2014 in Brazil and Malaysia, including seven from which we recovered full-length genomes. Of these, six represent the first full-length paramyxovirid genomes sequenced from the Americas, including two that are the first full-length bat morbillivirus genome sequences published to date. Our findings add to the vast number of viral sequences in public repositories, which have been increasing considerably in recent years due to the rising accessibility of metagenomics. Taxonomic classification of these sequences in the absence of phenotypic data has been a significant challenge, particularly in the subfamily Orthoparamyxovirinae, where the rate of discovery of novel sequences has been substantial. Using pairwise amino acid sequence classification (PAASC), we propose that five of these sequences belong to members of the genus Jeilongvirus and two belong to members of the genus Morbillivirus. We also highlight inconsistencies in the classification of Tupaia virus and Mòjiāng virus using the same demarcation criteria and suggest reclassification of these viruses into new genera. Importantly, this study underscores the critical importance of sequence length in PAASC analysis as well as the importance of biological characteristics such as genome organization in the taxonomic classification of viral sequences.

Discovery and Evolutionary Analysis of a Novel Bat-Borne Paramyxovirus

Paramyxoviruses are a group of RNA viruses, such as mumps virus, measles virus, Nipah virus, Hendra virus, Newcastle disease virus, and parainfluenza virus, usually transmitted by airborne droplets that are predominantly responsible for acute respiratory diseases. In this paper, we identified a novel paramyxovirus belonging to genus Jeilongvirus infecting 4/112 (3.6%) bats from two trapping sites of Hainan Province of China. In these animals, the viral RNA was detected exclusively in kidney tissues. This is the first full-length Jeilongvirus genome (18,095 nucleotides) from bats of genus Hipposideros, which exhibits a canonical genome organization and encodes SH and TM proteins. Results, based on phylogenic analysis and genetic distances, indicate that the novel paramyxovirus formed an independent lineage belonging to genus Jeilongvirus, representing, thus, a novel species. In addition, the virus-host macro-evolutionary analysis revealed that host-switching was not only a common co-phylogenetic event, but also a potential mechanism by which rats are infected by bat-origin Jeilongvirus through cross-species virus transmission, indicating a bat origin of the genus Jeilongvirus. Overall, our study broadens the viral diversity, geographical distribution, host range, and evolution of genus Jeilongvirus.

Hedgehogs as a Potential Source of Zoonotic Pathogens-A Review and an Update of Knowledge

Simple Summary

Up to date studies indicate that wild hedgehogs may act as carriers and/or hosts for bacterial, viral, and fungal pathogens with zoonotic potential, posing a significant threat to humans. The same applies to domestic hedgehogs, which are increasingly kept as pets. Considering the potential risk of infection to humans through close contact with hedgehogs or the contaminated environment they inhabit, current data on the prevalence of various zoonotic pathogens in these animals is desirable.

Abstract

Hedgehogs are small insectivorous mammals common across Europe, Asia, and Africa. The increased encroachment of humans into hedgehog habitats has disrupted the human-animal-environment interface. With growing interest in the zoonotic diseases of wildlife species, more studies have been devoted to this subject in the last few years. These papers provide information about known and new emerging diseases. Here we review the current knowledge regarding bacterial, viral, protozoic, and mycotic pathogens with zoonotic potential and assess the importance of hedgehogs as their carriers. Both wild and pet hedgehogs were included in the review. Data from several countries and various hedgehog species were included. The study shows the importance of hedgehogs as carriers of zoonotic diseases and reservoirs of zoonotic pathogens in varied habitats.

Genome Sequence of Ruloma Virus, a Novel Paramyxovirus Clustering Basally to Members of the Genus Jeilongvirus

We report here the complete genome sequence of ruloma virus, a novel paramyxovirus detected in a Machangu’s brush-furred rat from Tanzania. Ruloma virus has the longest orthoparamyxovirus genome reported to date and forms a sister clade to all currently known members of the genus Jeilongvirus.

We report here the complete genome sequence of ruloma virus, a novel paramyxovirus detected in a Machangu’s brush-furred rat from Tanzania. Ruloma virus has the longest orthoparamyxovirus genome reported to date and forms a sister clade to all currently known members of the genus Jeilongvirus.