Novel Arterivirus Associated with Outbreak of Fatal Encephalitis in European Hedgehogs, England, 2019

Genomic RNA recombination of porcine reproductive and respiratory syndrome virus and other arteriviruses

Arteriviruses in the Nidovirales order are single-stranded positive-sense RNA viruses infecting mammals. Arteriviruses are recognized for causing various clinical diseases, ranging from asymptomatic infections to severe conditions like respiratory syndromes and viral hemorrhagic fever. Notably, arteriviruses exhibit a high frequency of RNA recombination, and their robust recombination rates are a crucial factor in recurrent outbreaks. The recombination events also shape the countermeasures employed by arteriviruses during virus-host co-evolution and confer specific evolutionary benefits to viruses, implicating a role as a selective advantage in viral adaptation. This review delves into the molecular basis of RNA recombination in arteriviruses, the bioinformatics tools and methodologies used to visualize evolutionary relationships, and the identification of recombination breakpoints. Significant recombination events are highlighted for PRRSV and other arteriviruses, illustrating the profound implications of recombination for viral evolution and pathogenesis. Recombination between field viruses and between field viruses and vaccine strains can generate new variants with altered antigenic profiles and virulence, leading to diagnostic failure, severe clinical outcomes, and reduced vaccine efficacy. Despite the advances, further research is needed to understand recombination rates and hotspots, as well as to develop potential antiviral strategies and diagnostic approaches for arteriviruses.

Colocalization of hedgehog arterivirus 1 (HhAV-1) and histologic lesions in the European hedgehog (Erinaceus europaeus) with neurological disease

The European hedgehog (Erinaceus europaeus) is a protected species of conservation concern in the UK. In recent years, there have been multiple incidents of fatal encephalitis in captive hedgehogs in wildlife rescue centers associated with the molecular detection of a hedgehog arterivirus (HhAV-1). However, it remains unclear whether the virus is the causative agent of the central nervous system (CNS) lesions. In a retrospective investigation using postmortem material from 7 captive hedgehogs with neurological disease, and a single hedgehog with previously identified meningoencephalitis, histologic examination was conducted in tandem with viral RNA in situ hybridization (ISH) to appraise tissue distribution of HhAV-1 and the colocalization with histologic lesions. ISH revealed multicellular tropism of HhAV-1 involving monocyte-macrophage and vascular endothelial cells, with viral RNA detected in multiple organs, likely due to endotheliotropism and viremia. In the CNS, encephalomyelitis was mild whilst viral RNA was abundant and widely distributed, particularly in the microglial population and localized to areas with glial nodules. Splenic lymphoid depletion was generally mild but was moderate to severe in 2 septicemic animals. Brain samples from 13 control hedgehogs, found dead in the wild due to predation/trauma, were also screened for HhAV-1, of which 8 tested positive by real-time reverse transcription polymerase chain reaction (RT-PCR) with a low viral load. No CNS lesions or ISH labeling was observed in 2 of these control hedgehogs that could be examined histologically. Combined, these findings indicate that HhAV-1 infections in captive hedgehogs in English wildlife rescue centers may be associated with histopathologic alterations and clinical neurological disease.

Wildlife nidoviruses: biology, epidemiology, and disease associations of selected nidoviruses of mammals and reptiles

Wildlife is the source of many emerging infectious diseases. Several viruses from the order Nidovirales have recently emerged in wildlife, sometimes with severe consequences for endangered species. The order Nidovirales is currently classified into eight suborders, three of which contain viruses of vertebrates. Vertebrate coronaviruses (suborder Cornidovirineae) have been extensively studied, yet the other major suborders have received less attention. The aim of this minireview was to summarize the key findings from the published literature on nidoviruses of vertebrate wildlife from two suborders: Arnidovirineae and Tornidovirineae. These viruses were identified either during investigations of disease outbreaks or through molecular surveys of wildlife viromes, and include pathogens of reptiles and mammals. The available data on key biological features, disease associations, and pathology are presented, in addition to data on the frequency of infections among various host populations, and putative routes of transmission. While nidoviruses discussed here appear to have a restricted in vivo host range, little is known about their natural life cycle. Observational field-based studies outside of the mortality events are needed to facilitate an understanding of the virus-host-environment interactions that lead to the outbreaks. Laboratory-based studies are needed to understand the pathogenesis of diseases caused by novel nidoviruses and their evolutionary histories. Barriers preventing research progress include limited funding and the unavailability of virus- and host-specific reagents. To reduce mortalities in wildlife and further population declines, proactive development of expertise, technologies, and networks should be developed. These steps would enable effective management of future outbreaks and support wildlife conservation.

Novel Rodent Arterivirus Detected in the Brazilian Amazon

As part of a continuous effort to investigate the viral communities associated with wild mammals at the human-animal interface in an Amazonian metropolitan region, this study describes the detection of a novel rodent-borne arterivirus. A sample containing pooled organs of Oecomys paricola was submitted to RNA sequencing, and four sequences taxonomically assigned as related to the Arteriviridae family were recovered, corresponding to an almost complete genome of nearly 13 kb summed. In the phylogenetic analysis with the standard domains used for taxa demarcation in the family, the tentatively named Oecomys arterivirus 1 (OAV-1) was placed within the clade of rodent- and porcine-associated viruses, corresponding to the Variarterivirinae subfamily. The divergence analysis, based on the same amino acid alignment, corroborated the hypothesis that the virus may represent a new genus within the subfamily. These findings contribute to the expansion of the current knowledge about the diversity, host and geographical range of the viral family. Arterivirids are non-human pathogens and are usually species-specific, but the susceptibility of cell lines derived from different organisms should be conducted to confirm these statements for this proposed new genus in an initial attempt to assess its spillover potential.

Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses

Recent years have witnessed the discovery of several new viruses belonging to the family Arteriviridae, expanding the known diversity and host range of this group of complex RNA viruses. Although the pathological relevance of these new viruses is not always clear, several well-studied members of the family Arteriviridae are known to be important animal pathogens. Here, we report the complete genome sequences of four new arterivirus variants, belonging to two putative novel species. These new arteriviruses were discovered in African rodents and were given the names Lopma virus and Praja virus. Their genomes follow the characteristic genome organization of all known arteriviruses, even though they are only distantly related to currently known rodent-borne arteriviruses. Phylogenetic analysis shows that Lopma virus clusters in the subfamily Variarterivirinae, while Praja virus clusters near members of the subfamily Heroarterivirinae: the yet undescribed forest pouched giant rat arterivirus and hedgehog arterivirus 1. A co-divergence analysis of rodent-borne arteriviruses confirms that they share similar phylogenetic patterns with their hosts, with only very few cases of host shifting events throughout their evolutionary history. Overall, the genomes described here and their unique clustering with other arteriviruses further illustrate the existence of multiple rodent-borne arterivirus lineages, expanding our knowledge of the evolutionary origin of these viruses.